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- .gitattributes +1 -0
- 4AA-large/README.md +55 -0
- 4AA-large/test/AAAY-traj-arrays.npz +3 -0
- 4AA-large/test/AAAY-traj-state0.pdb +57 -0
- 4AA-large/test/AACE-traj-arrays.npz +3 -0
- 4AA-large/test/AACE-traj-state0.pdb +52 -0
- 4AA-large/test/AAEW-traj-arrays.npz +3 -0
- 4AA-large/test/AAEW-traj-state0.pdb +65 -0
- 4AA-large/test/AAGE-traj-arrays.npz +3 -0
- 4AA-large/test/AAGE-traj-state0.pdb +48 -0
- 4AA-large/test/AASK-traj-state0.pdb +59 -0
- 4AA-large/test/ACAK-traj-arrays.npz +3 -0
- 4AA-large/test/ACAK-traj-state0.pdb +59 -0
- 4AA-large/test/ACKY-traj-arrays.npz +3 -0
- 4AA-large/test/ACKY-traj-state0.pdb +70 -0
- 4AA-large/test/ADAS-traj-arrays.npz +3 -0
- 4AA-large/test/ADAS-traj-state0.pdb +49 -0
- 4AA-large/test/ADLL-traj-arrays.npz +3 -0
- 4AA-large/test/ADLL-traj-state0.pdb +66 -0
- 4AA-large/test/ADVF-traj-arrays.npz +3 -0
- 4AA-large/test/ADVF-traj-state0.pdb +64 -0
- 4AA-large/test/ADVK-traj-arrays.npz +3 -0
- 4AA-large/test/ADVK-traj-state0.pdb +66 -0
- 4AA-large/test/AEIS-traj-arrays.npz +3 -0
- 4AA-large/test/AEIS-traj-state0.pdb +61 -0
- 4AA-large/test/AEME-traj-arrays.npz +3 -0
- 4AA-large/test/AEME-traj-state0.pdb +63 -0
- 4AA-large/test/AEVI-traj-arrays.npz +3 -0
- 4AA-large/test/AEVI-traj-state0.pdb +66 -0
- 4AA-large/test/AFIA-traj-arrays.npz +3 -0
- 4AA-large/test/AFIA-traj-state0.pdb +65 -0
- 4AA-large/test/AFPN-traj-arrays.npz +3 -0
- 4AA-large/test/AFPN-traj-state0.pdb +64 -0
- 4AA-large/test/AGAK-traj-arrays.npz +3 -0
- 4AA-large/test/AGAK-traj-state0.pdb +55 -0
- 4AA-large/test/AHSH-traj-arrays.npz +3 -0
- 4AA-large/test/AHSH-traj-state0.pdb +61 -0
- 4AA-large/test/AIAV-traj-state0.pdb +61 -0
- 4AA-large/test/AKFR-traj-state0.pdb +82 -0
- 4AA-large/test/AKSL-traj-arrays.npz +3 -0
- 4AA-large/test/AKSL-traj-state0.pdb +68 -0
- 4AA-large/test/ALEF-traj-state0.pdb +70 -0
- 4AA-large/test/ALTQ-traj-arrays.npz +3 -0
- 4AA-large/test/ALTQ-traj-state0.pdb +66 -0
- 4AA-large/test/ALTV-traj-arrays.npz +3 -0
- 4AA-large/test/ALTV-traj-state0.pdb +65 -0
- 4AA-large/test/ALVE-traj-state0.pdb +66 -0
- 4AA-large/test/AMIG-traj-arrays.npz +3 -0
- 4AA-large/test/AMIG-traj-state0.pdb +59 -0
- 4AA-large/test/ANFG-traj-arrays.npz +3 -0
.gitattributes
CHANGED
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@@ -54,3 +54,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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*.jpeg filter=lfs diff=lfs merge=lfs -text
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*.webp filter=lfs diff=lfs merge=lfs -text
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4AA-huge/val/LIGY-traj.chk-sim.pickle.gz.old filter=lfs diff=lfs merge=lfs -text
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*.jpeg filter=lfs diff=lfs merge=lfs -text
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*.webp filter=lfs diff=lfs merge=lfs -text
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4AA-huge/val/LIGY-traj.chk-sim.pickle.gz.old filter=lfs diff=lfs merge=lfs -text
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4AA-large/val/SEKQ-traj.chk-sim.pickle.gz.old filter=lfs diff=lfs merge=lfs -text
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4AA-large/README.md
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# 4AA-large "Four Amino Acid" data set, tetrapeptides
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The difference to the 4AA data set is the much longer simulation time.
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This folder contains a data set of all-atom molecular dynamics trajectories for
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2333 tetrapeptides, i.e. small proteins composed of four amino acids.
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The data set is split into 1500 tetra-peptides in the train set, 400 in validation, and 433 in test.
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Each peptide in the train set is simulated for 50ns using classical molecular dynamics and the
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water is simulated using an implicit water model. Each other peptide is simulated for 500ns.
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For each trajectory two files are available:
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* `protein-state0.pdb`: contains the topology and initial 3D XYZ coordinates.
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* `protein-arrays.npz`: contains trajectory information.
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## NPZ Information
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Each NPZ file contains detailed information for a subset of simulation steps.
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There are T such frames and each NPZ file contains the following arrays:
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* 'step': `(T,)` array, Md step number.
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* 'energies': `(T,2)` array, each row containing [potential, kinetic] energies
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in kJ/mol.
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* 'positions': `(T,num_atoms,3)` array, positions in nm.
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* 'velocities': `(T,num_atoms,3)` array, velocities in nm/ps.
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* 'forces': `(T,num_atoms,3)` array, forces in kJ/(mol nm).
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## Dataset construction
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The dataset was constructed in the following way:
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1. For all included PDB files, perform a molecular
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dynamics simulation:
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a.) Use OpenMM with the AMBER14 force field and implicit water (`preset=amber14-implicit`).`
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b.) Perform an energy minimization (relaxation) from the initial PDB
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configuration.
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c.) Use a Langevin integrator at temperature T=310K, friction=0.3/ps,
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timestep=0.5fs for 2e6 steps to equilibriate ("burn-in phase").
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d.) Use a Langevin integrator at temperature T=310K, friction=0.3/ps,
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timestep=0.5fs for 1e8/1e9 steps to sample a trajectory ("sample phase").
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2. Save trajectory information every 10,000 steps (5ps) to an `arrays.npz`
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file.
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## Credit and Authors
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This dataset was created in September 2022 as part of the Molecular Simulation
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initiative.
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4AA-large/test/AAAY-traj-arrays.npz
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version https://git-lfs.github.com/spec/v1
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oid sha256:b231d58f5ca9487bef5c7eec174822d1caf3f6e09ad8bbd192cf721898658c06
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size 90730841
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4AA-large/test/AAAY-traj-state0.pdb
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REMARK 1 CREATED WITH OPENMM 7.7, 2022-08-29
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ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
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| 3 |
+
ATOM 2 H2 ALA A 1 2.494 1.311 0.837 1.00 0.00 H
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+
ATOM 3 H3 ALA A 1 2.645 1.448 -0.990 1.00 0.00 H
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+
ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
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+
ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
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+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
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+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
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+
ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
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| 10 |
+
ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
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ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
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+
ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
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| 13 |
+
ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
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+
ATOM 13 N ALA A 2 6.191 3.839 0.000 1.00 0.00 N
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| 15 |
+
ATOM 14 H ALA A 2 5.715 4.730 0.000 1.00 0.00 H
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+
ATOM 15 CA ALA A 2 7.640 3.839 0.000 1.00 0.00 C
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+
ATOM 16 HA ALA A 2 8.004 3.325 0.890 1.00 0.00 H
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ATOM 17 CB ALA A 2 8.189 3.127 -1.232 1.00 0.00 C
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+
ATOM 18 HB1 ALA A 2 7.841 3.636 -2.131 1.00 0.00 H
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ATOM 19 HB2 ALA A 2 9.279 3.142 -1.206 1.00 0.00 H
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+
ATOM 20 HB3 ALA A 2 7.841 2.094 -1.241 1.00 0.00 H
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+
ATOM 21 C ALA A 2 8.188 5.259 0.000 1.00 0.00 C
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+
ATOM 22 O ALA A 2 7.425 6.222 0.000 1.00 0.00 O
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ATOM 23 N ALA A 3 9.517 5.386 0.000 1.00 0.00 N
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+
ATOM 24 H ALA A 3 10.103 4.564 0.000 1.00 0.00 H
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| 26 |
+
ATOM 25 CA ALA A 3 10.161 6.684 0.000 1.00 0.00 C
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+
ATOM 26 HA ALA A 3 9.863 7.239 -0.890 1.00 0.00 H
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ATOM 27 CB ALA A 3 9.768 7.492 1.232 1.00 0.00 C
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ATOM 28 HB1 ALA A 3 10.068 6.954 2.131 1.00 0.00 H
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ATOM 29 HB2 ALA A 3 10.266 8.462 1.206 1.00 0.00 H
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ATOM 30 HB3 ALA A 3 8.688 7.640 1.241 1.00 0.00 H
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ATOM 31 C ALA A 3 11.677 6.544 0.000 1.00 0.00 C
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+
ATOM 32 O ALA A 3 12.200 5.432 0.000 1.00 0.00 O
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ATOM 33 N TYR A 4 12.382 7.677 0.000 1.00 0.00 N
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ATOM 34 H TYR A 4 11.906 8.568 0.000 1.00 0.00 H
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+
ATOM 35 CA TYR A 4 13.831 7.677 0.000 1.00 0.00 C
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ATOM 36 HA TYR A 4 14.195 7.163 0.890 1.00 0.00 H
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ATOM 37 CB TYR A 4 14.380 6.966 -1.232 1.00 0.00 C
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ATOM 38 HB2 TYR A 4 14.032 5.933 -1.241 1.00 0.00 H
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ATOM 39 HB3 TYR A 4 14.032 7.474 -2.131 1.00 0.00 H
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ATOM 40 CG TYR A 4 15.889 6.987 -1.195 1.00 0.00 C
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ATOM 41 CD1 TYR A 4 16.624 6.391 -2.227 1.00 0.00 C
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ATOM 42 HD1 TYR A 4 16.106 5.912 -3.058 1.00 0.00 H
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ATOM 43 CE1 TYR A 4 18.023 6.411 -2.193 1.00 0.00 C
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ATOM 44 HE1 TYR A 4 18.595 5.947 -2.997 1.00 0.00 H
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ATOM 45 CZ TYR A 4 18.688 7.027 -1.126 1.00 0.00 C
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ATOM 46 OH TYR A 4 20.048 7.046 -1.092 1.00 0.00 O
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ATOM 47 HH TYR A 4 20.448 6.610 -1.848 1.00 0.00 H
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ATOM 48 CE2 TYR A 4 17.954 7.623 -0.094 1.00 0.00 C
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ATOM 49 HE2 TYR A 4 18.472 8.103 0.737 1.00 0.00 H
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ATOM 50 CD2 TYR A 4 16.555 7.603 -0.128 1.00 0.00 C
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+
ATOM 51 HD2 TYR A 4 15.983 8.067 0.676 1.00 0.00 H
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ATOM 52 C TYR A 4 14.379 9.097 0.000 1.00 0.00 C
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+
ATOM 53 O TYR A 4 13.616 10.060 0.000 1.00 0.00 O
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+
ATOM 54 OXT TYR A 4 15.661 9.063 0.075 1.00 0.00 O
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TER 55 TYR A 4
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END
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4AA-large/test/AACE-traj-arrays.npz
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version https://git-lfs.github.com/spec/v1
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oid sha256:ca33564f8df31538495f7e6f8a77d8153fbd89d71fcc301fb14124e5e73ef548
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size 822669285
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4AA-large/test/AACE-traj-state0.pdb
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| 1 |
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REMARK 1 CREATED WITH OPENMM 7.7, 2022-08-30
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| 2 |
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ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
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| 3 |
+
ATOM 2 H2 ALA A 1 2.492 1.313 0.836 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.645 1.451 -0.989 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
|
| 11 |
+
ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 12 |
+
ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 13 |
+
ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 14 |
+
ATOM 13 N ALA A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H ALA A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA ALA A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA ALA A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 CB ALA A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 19 |
+
ATOM 18 HB1 ALA A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 20 |
+
ATOM 19 HB2 ALA A 2 9.279 3.142 -1.206 1.00 0.00 H
|
| 21 |
+
ATOM 20 HB3 ALA A 2 7.841 2.094 -1.241 1.00 0.00 H
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| 22 |
+
ATOM 21 C ALA A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 23 |
+
ATOM 22 O ALA A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 24 |
+
ATOM 23 N CYS A 3 9.517 5.386 0.000 1.00 0.00 N
|
| 25 |
+
ATOM 24 H CYS A 3 10.103 4.564 0.000 1.00 0.00 H
|
| 26 |
+
ATOM 25 CA CYS A 3 10.161 6.684 0.000 1.00 0.00 C
|
| 27 |
+
ATOM 26 HA CYS A 3 9.863 7.239 -0.890 1.00 0.00 H
|
| 28 |
+
ATOM 27 CB CYS A 3 9.768 7.492 1.232 1.00 0.00 C
|
| 29 |
+
ATOM 28 HB2 CYS A 3 8.688 7.640 1.241 1.00 0.00 H
|
| 30 |
+
ATOM 29 HB3 CYS A 3 10.068 6.954 2.131 1.00 0.00 H
|
| 31 |
+
ATOM 30 SG CYS A 3 10.501 9.142 1.366 1.00 0.00 S
|
| 32 |
+
ATOM 31 HG CYS A 3 9.916 9.461 2.518 1.00 0.00 H
|
| 33 |
+
ATOM 32 C CYS A 3 11.677 6.544 0.000 1.00 0.00 C
|
| 34 |
+
ATOM 33 O CYS A 3 12.200 5.432 0.000 1.00 0.00 O
|
| 35 |
+
ATOM 34 N GLU A 4 12.382 7.677 0.000 1.00 0.00 N
|
| 36 |
+
ATOM 35 H GLU A 4 11.906 8.568 0.000 1.00 0.00 H
|
| 37 |
+
ATOM 36 CA GLU A 4 13.831 7.677 0.000 1.00 0.00 C
|
| 38 |
+
ATOM 37 HA GLU A 4 14.195 7.163 0.890 1.00 0.00 H
|
| 39 |
+
ATOM 38 CB GLU A 4 14.380 6.966 -1.232 1.00 0.00 C
|
| 40 |
+
ATOM 39 HB2 GLU A 4 14.032 5.933 -1.241 1.00 0.00 H
|
| 41 |
+
ATOM 40 HB3 GLU A 4 14.032 7.474 -2.131 1.00 0.00 H
|
| 42 |
+
ATOM 41 CG GLU A 4 15.889 6.987 -1.195 1.00 0.00 C
|
| 43 |
+
ATOM 42 HG2 GLU A 4 16.238 8.020 -1.186 1.00 0.00 H
|
| 44 |
+
ATOM 43 HG3 GLU A 4 16.238 6.479 -0.296 1.00 0.00 H
|
| 45 |
+
ATOM 44 CD GLU A 4 16.439 6.275 -2.429 1.00 0.00 C
|
| 46 |
+
ATOM 45 OE1 GLU A 4 16.646 6.977 -3.454 1.00 0.00 O
|
| 47 |
+
ATOM 46 OE2 GLU A 4 16.646 5.036 -2.334 1.00 0.00 O
|
| 48 |
+
ATOM 47 C GLU A 4 14.379 9.097 0.000 1.00 0.00 C
|
| 49 |
+
ATOM 48 O GLU A 4 13.616 10.060 0.000 1.00 0.00 O
|
| 50 |
+
ATOM 49 OXT GLU A 4 15.665 9.052 0.060 1.00 0.00 O
|
| 51 |
+
TER 50 GLU A 4
|
| 52 |
+
END
|
4AA-large/test/AAEW-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:382bfe31201f3567f420b6f1762630b90b56dee34ab044c259b3810c4a0b0754
|
| 3 |
+
size 1037739342
|
4AA-large/test/AAEW-traj-state0.pdb
ADDED
|
@@ -0,0 +1,65 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH OPENMM 7.7, 2022-08-30
|
| 2 |
+
ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ALA A 1 2.504 1.310 0.847 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.632 1.450 -0.980 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
|
| 11 |
+
ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 12 |
+
ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 13 |
+
ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 14 |
+
ATOM 13 N ALA A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H ALA A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA ALA A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA ALA A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 CB ALA A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 19 |
+
ATOM 18 HB1 ALA A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 20 |
+
ATOM 19 HB2 ALA A 2 9.279 3.142 -1.206 1.00 0.00 H
|
| 21 |
+
ATOM 20 HB3 ALA A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 22 |
+
ATOM 21 C ALA A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 23 |
+
ATOM 22 O ALA A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 24 |
+
ATOM 23 N GLU A 3 9.517 5.386 0.000 1.00 0.00 N
|
| 25 |
+
ATOM 24 H GLU A 3 10.103 4.564 0.000 1.00 0.00 H
|
| 26 |
+
ATOM 25 CA GLU A 3 10.161 6.684 0.000 1.00 0.00 C
|
| 27 |
+
ATOM 26 HA GLU A 3 9.863 7.239 -0.890 1.00 0.00 H
|
| 28 |
+
ATOM 27 CB GLU A 3 9.768 7.492 1.232 1.00 0.00 C
|
| 29 |
+
ATOM 28 HB2 GLU A 3 8.688 7.640 1.241 1.00 0.00 H
|
| 30 |
+
ATOM 29 HB3 GLU A 3 10.068 6.954 2.131 1.00 0.00 H
|
| 31 |
+
ATOM 30 CG GLU A 3 10.458 8.835 1.195 1.00 0.00 C
|
| 32 |
+
ATOM 31 HG2 GLU A 3 11.538 8.688 1.186 1.00 0.00 H
|
| 33 |
+
ATOM 32 HG3 GLU A 3 10.158 9.374 0.296 1.00 0.00 H
|
| 34 |
+
ATOM 33 CD GLU A 3 10.065 9.644 2.429 1.00 0.00 C
|
| 35 |
+
ATOM 34 OE1 GLU A 3 10.786 9.518 3.454 1.00 0.00 O
|
| 36 |
+
ATOM 35 OE2 GLU A 3 9.047 10.381 2.334 1.00 0.00 O
|
| 37 |
+
ATOM 36 C GLU A 3 11.677 6.544 0.000 1.00 0.00 C
|
| 38 |
+
ATOM 37 O GLU A 3 12.200 5.432 0.000 1.00 0.00 O
|
| 39 |
+
ATOM 38 N TRP A 4 12.382 7.677 0.000 1.00 0.00 N
|
| 40 |
+
ATOM 39 H TRP A 4 11.906 8.568 0.000 1.00 0.00 H
|
| 41 |
+
ATOM 40 CA TRP A 4 13.831 7.677 0.000 1.00 0.00 C
|
| 42 |
+
ATOM 41 HA TRP A 4 14.195 7.163 0.890 1.00 0.00 H
|
| 43 |
+
ATOM 42 CB TRP A 4 14.380 6.966 -1.232 1.00 0.00 C
|
| 44 |
+
ATOM 43 HB2 TRP A 4 14.032 5.933 -1.241 1.00 0.00 H
|
| 45 |
+
ATOM 44 HB3 TRP A 4 14.032 7.474 -2.131 1.00 0.00 H
|
| 46 |
+
ATOM 45 CG TRP A 4 15.887 6.914 -1.321 1.00 0.00 C
|
| 47 |
+
ATOM 46 CD1 TRP A 4 16.618 6.353 -2.293 1.00 0.00 C
|
| 48 |
+
ATOM 47 HD1 TRP A 4 16.125 5.867 -3.135 1.00 0.00 H
|
| 49 |
+
ATOM 48 NE1 TRP A 4 17.992 6.551 -1.950 1.00 0.00 N
|
| 50 |
+
ATOM 49 HE1 TRP A 4 18.784 6.238 -2.493 1.00 0.00 H
|
| 51 |
+
ATOM 50 CE2 TRP A 4 18.058 7.206 -0.817 1.00 0.00 C
|
| 52 |
+
ATOM 51 CZ2 TRP A 4 19.204 7.608 -0.120 1.00 0.00 C
|
| 53 |
+
ATOM 52 HZ2 TRP A 4 20.193 7.379 -0.517 1.00 0.00 H
|
| 54 |
+
ATOM 53 CH2 TRP A 4 18.984 8.294 1.069 1.00 0.00 C
|
| 55 |
+
ATOM 54 HH2 TRP A 4 19.830 8.638 1.664 1.00 0.00 H
|
| 56 |
+
ATOM 55 CZ3 TRP A 4 17.731 8.546 1.505 1.00 0.00 C
|
| 57 |
+
ATOM 56 HZ3 TRP A 4 17.578 9.086 2.440 1.00 0.00 H
|
| 58 |
+
ATOM 57 CE3 TRP A 4 16.592 8.131 0.786 1.00 0.00 C
|
| 59 |
+
ATOM 58 HE3 TRP A 4 15.596 8.352 1.168 1.00 0.00 H
|
| 60 |
+
ATOM 59 CD2 TRP A 4 16.814 7.440 -0.412 1.00 0.00 C
|
| 61 |
+
ATOM 60 C TRP A 4 14.379 9.097 0.000 1.00 0.00 C
|
| 62 |
+
ATOM 61 O TRP A 4 13.616 10.060 0.000 1.00 0.00 O
|
| 63 |
+
ATOM 62 OXT TRP A 4 15.656 9.066 0.025 1.00 0.00 O
|
| 64 |
+
TER 63 TRP A 4
|
| 65 |
+
END
|
4AA-large/test/AAGE-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:62a79816b80fced349699233d8aa6ee2708d746e98545b37592c379acb40f89d
|
| 3 |
+
size 756559270
|
4AA-large/test/AAGE-traj-state0.pdb
ADDED
|
@@ -0,0 +1,48 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH OPENMM 7.7, 2022-08-30
|
| 2 |
+
ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ALA A 1 2.495 1.308 0.837 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.645 1.451 -0.989 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
|
| 11 |
+
ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 12 |
+
ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 13 |
+
ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 14 |
+
ATOM 13 N ALA A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H ALA A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA ALA A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA ALA A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 CB ALA A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 19 |
+
ATOM 18 HB1 ALA A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 20 |
+
ATOM 19 HB2 ALA A 2 9.279 3.142 -1.206 1.00 0.00 H
|
| 21 |
+
ATOM 20 HB3 ALA A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 22 |
+
ATOM 21 C ALA A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 23 |
+
ATOM 22 O ALA A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 24 |
+
ATOM 23 N GLY A 3 9.517 5.386 0.000 1.00 0.00 N
|
| 25 |
+
ATOM 24 H GLY A 3 10.103 4.564 0.000 1.00 0.00 H
|
| 26 |
+
ATOM 25 CA GLY A 3 10.161 6.684 0.000 1.00 0.00 C
|
| 27 |
+
ATOM 26 HA2 GLY A 3 9.863 7.239 -0.890 1.00 0.00 H
|
| 28 |
+
ATOM 27 HA3 GLY A 3 9.863 7.239 0.890 1.00 0.00 H
|
| 29 |
+
ATOM 28 C GLY A 3 11.675 6.525 0.000 1.00 0.00 C
|
| 30 |
+
ATOM 29 O GLY A 3 12.184 5.407 0.000 1.00 0.00 O
|
| 31 |
+
ATOM 30 N GLU A 4 12.394 7.650 0.000 1.00 0.00 N
|
| 32 |
+
ATOM 31 H GLU A 4 11.929 8.547 0.000 1.00 0.00 H
|
| 33 |
+
ATOM 32 CA GLU A 4 13.843 7.632 0.000 1.00 0.00 C
|
| 34 |
+
ATOM 33 HA GLU A 4 14.200 7.114 0.890 1.00 0.00 H
|
| 35 |
+
ATOM 34 CB GLU A 4 14.383 6.914 -1.232 1.00 0.00 C
|
| 36 |
+
ATOM 35 HB2 GLU A 4 14.022 5.886 -1.241 1.00 0.00 H
|
| 37 |
+
ATOM 36 HB3 GLU A 4 14.041 7.427 -2.131 1.00 0.00 H
|
| 38 |
+
ATOM 37 CG GLU A 4 15.893 6.917 -1.195 1.00 0.00 C
|
| 39 |
+
ATOM 38 HG2 GLU A 4 16.254 7.945 -1.186 1.00 0.00 H
|
| 40 |
+
ATOM 39 HG3 GLU A 4 16.236 6.404 -0.296 1.00 0.00 H
|
| 41 |
+
ATOM 40 CD GLU A 4 16.434 6.198 -2.429 1.00 0.00 C
|
| 42 |
+
ATOM 41 OE1 GLU A 4 16.650 6.898 -3.454 1.00 0.00 O
|
| 43 |
+
ATOM 42 OE2 GLU A 4 16.626 4.957 -2.334 1.00 0.00 O
|
| 44 |
+
ATOM 43 C GLU A 4 14.408 9.045 0.000 1.00 0.00 C
|
| 45 |
+
ATOM 44 O GLU A 4 13.657 10.018 0.000 1.00 0.00 O
|
| 46 |
+
ATOM 45 OXT GLU A 4 15.693 8.981 0.068 1.00 0.00 O
|
| 47 |
+
TER 46 GLU A 4
|
| 48 |
+
END
|
4AA-large/test/AASK-traj-state0.pdb
ADDED
|
@@ -0,0 +1,59 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH OPENMM 7.7, 2022-09-01
|
| 2 |
+
ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ALA A 1 2.493 1.316 0.838 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.639 1.454 -0.986 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
|
| 11 |
+
ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 12 |
+
ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 13 |
+
ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 14 |
+
ATOM 13 N ALA A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H ALA A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA ALA A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA ALA A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 CB ALA A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 19 |
+
ATOM 18 HB1 ALA A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 20 |
+
ATOM 19 HB2 ALA A 2 9.279 3.142 -1.206 1.00 0.00 H
|
| 21 |
+
ATOM 20 HB3 ALA A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 22 |
+
ATOM 21 C ALA A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 23 |
+
ATOM 22 O ALA A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 24 |
+
ATOM 23 N SER A 3 9.517 5.386 0.000 1.00 0.00 N
|
| 25 |
+
ATOM 24 H SER A 3 10.103 4.564 0.000 1.00 0.00 H
|
| 26 |
+
ATOM 25 CA SER A 3 10.161 6.684 0.000 1.00 0.00 C
|
| 27 |
+
ATOM 26 HA SER A 3 9.863 7.239 -0.890 1.00 0.00 H
|
| 28 |
+
ATOM 27 CB SER A 3 9.768 7.492 1.232 1.00 0.00 C
|
| 29 |
+
ATOM 28 HB2 SER A 3 8.688 7.640 1.241 1.00 0.00 H
|
| 30 |
+
ATOM 29 HB3 SER A 3 10.068 6.954 2.131 1.00 0.00 H
|
| 31 |
+
ATOM 30 OG SER A 3 10.422 8.764 1.197 1.00 0.00 O
|
| 32 |
+
ATOM 31 HG SER A 3 10.174 9.272 1.973 1.00 0.00 H
|
| 33 |
+
ATOM 32 C SER A 3 11.677 6.544 0.000 1.00 0.00 C
|
| 34 |
+
ATOM 33 O SER A 3 12.200 5.432 0.000 1.00 0.00 O
|
| 35 |
+
ATOM 34 N LYS A 4 12.382 7.677 0.000 1.00 0.00 N
|
| 36 |
+
ATOM 35 H LYS A 4 11.906 8.568 0.000 1.00 0.00 H
|
| 37 |
+
ATOM 36 CA LYS A 4 13.831 7.677 0.000 1.00 0.00 C
|
| 38 |
+
ATOM 37 HA LYS A 4 14.195 7.163 0.890 1.00 0.00 H
|
| 39 |
+
ATOM 38 CB LYS A 4 14.380 6.966 -1.232 1.00 0.00 C
|
| 40 |
+
ATOM 39 HB2 LYS A 4 14.032 5.933 -1.241 1.00 0.00 H
|
| 41 |
+
ATOM 40 HB3 LYS A 4 14.032 7.474 -2.131 1.00 0.00 H
|
| 42 |
+
ATOM 41 CG LYS A 4 15.904 6.987 -1.195 1.00 0.00 C
|
| 43 |
+
ATOM 42 HG2 LYS A 4 16.253 8.020 -1.186 1.00 0.00 H
|
| 44 |
+
ATOM 43 HG3 LYS A 4 16.253 6.479 -0.296 1.00 0.00 H
|
| 45 |
+
ATOM 44 CD LYS A 4 16.453 6.276 -2.427 1.00 0.00 C
|
| 46 |
+
ATOM 45 HD2 LYS A 4 16.105 5.243 -2.436 1.00 0.00 H
|
| 47 |
+
ATOM 46 HD3 LYS A 4 16.105 6.785 -3.326 1.00 0.00 H
|
| 48 |
+
ATOM 47 CE LYS A 4 17.978 6.298 -2.389 1.00 0.00 C
|
| 49 |
+
ATOM 48 HE2 LYS A 4 18.327 7.330 -2.380 1.00 0.00 H
|
| 50 |
+
ATOM 49 HE3 LYS A 4 18.327 5.789 -1.491 1.00 0.00 H
|
| 51 |
+
ATOM 50 NZ LYS A 4 18.507 5.612 -3.577 1.00 0.00 N
|
| 52 |
+
ATOM 51 HZ1 LYS A 4 18.184 6.084 -4.410 1.00 0.00 H
|
| 53 |
+
ATOM 52 HZ2 LYS A 4 19.517 5.626 -3.552 1.00 0.00 H
|
| 54 |
+
ATOM 53 HZ3 LYS A 4 18.184 4.655 -3.585 1.00 0.00 H
|
| 55 |
+
ATOM 54 C LYS A 4 14.379 9.097 0.000 1.00 0.00 C
|
| 56 |
+
ATOM 55 O LYS A 4 13.616 10.060 0.000 1.00 0.00 O
|
| 57 |
+
ATOM 56 OXT LYS A 4 15.665 9.050 0.059 1.00 0.00 O
|
| 58 |
+
TER 57 LYS A 4
|
| 59 |
+
END
|
4AA-large/test/ACAK-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:34ff5d2c6d31a075f8c23eb173d313ea85c5c347cb0cd2473e8546c135dc93db
|
| 3 |
+
size 939593417
|
4AA-large/test/ACAK-traj-state0.pdb
ADDED
|
@@ -0,0 +1,59 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH OPENMM 7.7, 2022-09-02
|
| 2 |
+
ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ALA A 1 2.640 1.451 -0.986 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.493 1.311 0.836 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
|
| 11 |
+
ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 12 |
+
ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 13 |
+
ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 14 |
+
ATOM 13 N CYS A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H CYS A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA CYS A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA CYS A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 CB CYS A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 19 |
+
ATOM 18 HB2 CYS A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 20 |
+
ATOM 19 HB3 CYS A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 21 |
+
ATOM 20 SG CYS A 2 9.992 3.050 -1.366 1.00 0.00 S
|
| 22 |
+
ATOM 21 HG CYS A 2 10.018 2.385 -2.518 1.00 0.00 H
|
| 23 |
+
ATOM 22 C CYS A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 24 |
+
ATOM 23 O CYS A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 25 |
+
ATOM 24 N ALA A 3 9.517 5.386 0.000 1.00 0.00 N
|
| 26 |
+
ATOM 25 H ALA A 3 10.103 4.564 0.000 1.00 0.00 H
|
| 27 |
+
ATOM 26 CA ALA A 3 10.161 6.684 0.000 1.00 0.00 C
|
| 28 |
+
ATOM 27 HA ALA A 3 9.863 7.239 -0.890 1.00 0.00 H
|
| 29 |
+
ATOM 28 CB ALA A 3 9.768 7.492 1.232 1.00 0.00 C
|
| 30 |
+
ATOM 29 HB1 ALA A 3 10.068 6.954 2.131 1.00 0.00 H
|
| 31 |
+
ATOM 30 HB2 ALA A 3 10.266 8.462 1.206 1.00 0.00 H
|
| 32 |
+
ATOM 31 HB3 ALA A 3 8.688 7.640 1.241 1.00 0.00 H
|
| 33 |
+
ATOM 32 C ALA A 3 11.677 6.544 0.000 1.00 0.00 C
|
| 34 |
+
ATOM 33 O ALA A 3 12.200 5.432 0.000 1.00 0.00 O
|
| 35 |
+
ATOM 34 N LYS A 4 12.382 7.677 0.000 1.00 0.00 N
|
| 36 |
+
ATOM 35 H LYS A 4 11.906 8.568 0.000 1.00 0.00 H
|
| 37 |
+
ATOM 36 CA LYS A 4 13.831 7.677 0.000 1.00 0.00 C
|
| 38 |
+
ATOM 37 HA LYS A 4 14.195 7.163 0.890 1.00 0.00 H
|
| 39 |
+
ATOM 38 CB LYS A 4 14.380 6.966 -1.232 1.00 0.00 C
|
| 40 |
+
ATOM 39 HB2 LYS A 4 14.032 5.933 -1.241 1.00 0.00 H
|
| 41 |
+
ATOM 40 HB3 LYS A 4 14.032 7.474 -2.131 1.00 0.00 H
|
| 42 |
+
ATOM 41 CG LYS A 4 15.904 6.987 -1.195 1.00 0.00 C
|
| 43 |
+
ATOM 42 HG2 LYS A 4 16.253 8.020 -1.186 1.00 0.00 H
|
| 44 |
+
ATOM 43 HG3 LYS A 4 16.253 6.479 -0.296 1.00 0.00 H
|
| 45 |
+
ATOM 44 CD LYS A 4 16.453 6.276 -2.427 1.00 0.00 C
|
| 46 |
+
ATOM 45 HD2 LYS A 4 16.105 5.243 -2.436 1.00 0.00 H
|
| 47 |
+
ATOM 46 HD3 LYS A 4 16.105 6.785 -3.326 1.00 0.00 H
|
| 48 |
+
ATOM 47 CE LYS A 4 17.978 6.298 -2.389 1.00 0.00 C
|
| 49 |
+
ATOM 48 HE2 LYS A 4 18.327 7.330 -2.380 1.00 0.00 H
|
| 50 |
+
ATOM 49 HE3 LYS A 4 18.327 5.789 -1.491 1.00 0.00 H
|
| 51 |
+
ATOM 50 NZ LYS A 4 18.507 5.612 -3.577 1.00 0.00 N
|
| 52 |
+
ATOM 51 HZ1 LYS A 4 18.184 6.084 -4.410 1.00 0.00 H
|
| 53 |
+
ATOM 52 HZ2 LYS A 4 19.517 5.626 -3.552 1.00 0.00 H
|
| 54 |
+
ATOM 53 HZ3 LYS A 4 18.184 4.655 -3.585 1.00 0.00 H
|
| 55 |
+
ATOM 54 C LYS A 4 14.379 9.097 0.000 1.00 0.00 C
|
| 56 |
+
ATOM 55 O LYS A 4 13.616 10.060 0.000 1.00 0.00 O
|
| 57 |
+
ATOM 56 OXT LYS A 4 15.665 9.049 0.063 1.00 0.00 O
|
| 58 |
+
TER 57 LYS A 4
|
| 59 |
+
END
|
4AA-large/test/ACKY-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:a059d8736388215ca250556a88583b141687d4c3dbbf70421ec7b92dd5ba7d39
|
| 3 |
+
size 1123810154
|
4AA-large/test/ACKY-traj-state0.pdb
ADDED
|
@@ -0,0 +1,70 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH OPENMM 7.7, 2022-09-01
|
| 2 |
+
ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ALA A 1 2.643 1.446 -0.987 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.495 1.311 0.839 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
|
| 11 |
+
ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 12 |
+
ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 13 |
+
ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 14 |
+
ATOM 13 N CYS A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H CYS A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA CYS A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA CYS A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 CB CYS A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 19 |
+
ATOM 18 HB2 CYS A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 20 |
+
ATOM 19 HB3 CYS A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 21 |
+
ATOM 20 SG CYS A 2 9.992 3.050 -1.366 1.00 0.00 S
|
| 22 |
+
ATOM 21 HG CYS A 2 10.018 2.385 -2.518 1.00 0.00 H
|
| 23 |
+
ATOM 22 C CYS A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 24 |
+
ATOM 23 O CYS A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 25 |
+
ATOM 24 N LYS A 3 9.517 5.386 0.000 1.00 0.00 N
|
| 26 |
+
ATOM 25 H LYS A 3 10.103 4.564 0.000 1.00 0.00 H
|
| 27 |
+
ATOM 26 CA LYS A 3 10.161 6.684 0.000 1.00 0.00 C
|
| 28 |
+
ATOM 27 HA LYS A 3 9.863 7.239 -0.890 1.00 0.00 H
|
| 29 |
+
ATOM 28 CB LYS A 3 9.768 7.492 1.232 1.00 0.00 C
|
| 30 |
+
ATOM 29 HB2 LYS A 3 8.688 7.640 1.241 1.00 0.00 H
|
| 31 |
+
ATOM 30 HB3 LYS A 3 10.068 6.954 2.131 1.00 0.00 H
|
| 32 |
+
ATOM 31 CG LYS A 3 10.465 8.848 1.195 1.00 0.00 C
|
| 33 |
+
ATOM 32 HG2 LYS A 3 11.545 8.702 1.186 1.00 0.00 H
|
| 34 |
+
ATOM 33 HG3 LYS A 3 10.165 9.387 0.296 1.00 0.00 H
|
| 35 |
+
ATOM 34 CD LYS A 3 10.072 9.656 2.427 1.00 0.00 C
|
| 36 |
+
ATOM 35 HD2 LYS A 3 8.992 9.803 2.436 1.00 0.00 H
|
| 37 |
+
ATOM 36 HD3 LYS A 3 10.373 9.118 3.326 1.00 0.00 H
|
| 38 |
+
ATOM 37 CE LYS A 3 10.769 11.012 2.389 1.00 0.00 C
|
| 39 |
+
ATOM 38 HE2 LYS A 3 11.849 10.866 2.380 1.00 0.00 H
|
| 40 |
+
ATOM 39 HE3 LYS A 3 10.469 11.551 1.491 1.00 0.00 H
|
| 41 |
+
ATOM 40 NZ LYS A 3 10.390 11.791 3.577 1.00 0.00 N
|
| 42 |
+
ATOM 41 HZ1 LYS A 3 10.669 11.292 4.410 1.00 0.00 H
|
| 43 |
+
ATOM 42 HZ2 LYS A 3 10.852 12.689 3.552 1.00 0.00 H
|
| 44 |
+
ATOM 43 HZ3 LYS A 3 9.390 11.927 3.585 1.00 0.00 H
|
| 45 |
+
ATOM 44 C LYS A 3 11.677 6.544 0.000 1.00 0.00 C
|
| 46 |
+
ATOM 45 O LYS A 3 12.200 5.432 0.000 1.00 0.00 O
|
| 47 |
+
ATOM 46 N TYR A 4 12.382 7.677 0.000 1.00 0.00 N
|
| 48 |
+
ATOM 47 H TYR A 4 11.906 8.568 0.000 1.00 0.00 H
|
| 49 |
+
ATOM 48 CA TYR A 4 13.831 7.677 0.000 1.00 0.00 C
|
| 50 |
+
ATOM 49 HA TYR A 4 14.195 7.163 0.890 1.00 0.00 H
|
| 51 |
+
ATOM 50 CB TYR A 4 14.380 6.966 -1.232 1.00 0.00 C
|
| 52 |
+
ATOM 51 HB2 TYR A 4 14.032 5.933 -1.241 1.00 0.00 H
|
| 53 |
+
ATOM 52 HB3 TYR A 4 14.032 7.474 -2.131 1.00 0.00 H
|
| 54 |
+
ATOM 53 CG TYR A 4 15.889 6.987 -1.195 1.00 0.00 C
|
| 55 |
+
ATOM 54 CD1 TYR A 4 16.624 6.391 -2.227 1.00 0.00 C
|
| 56 |
+
ATOM 55 HD1 TYR A 4 16.106 5.912 -3.058 1.00 0.00 H
|
| 57 |
+
ATOM 56 CE1 TYR A 4 18.023 6.411 -2.193 1.00 0.00 C
|
| 58 |
+
ATOM 57 HE1 TYR A 4 18.595 5.947 -2.997 1.00 0.00 H
|
| 59 |
+
ATOM 58 CZ TYR A 4 18.688 7.027 -1.126 1.00 0.00 C
|
| 60 |
+
ATOM 59 OH TYR A 4 20.048 7.046 -1.092 1.00 0.00 O
|
| 61 |
+
ATOM 60 HH TYR A 4 20.448 6.610 -1.848 1.00 0.00 H
|
| 62 |
+
ATOM 61 CE2 TYR A 4 17.954 7.623 -0.094 1.00 0.00 C
|
| 63 |
+
ATOM 62 HE2 TYR A 4 18.472 8.103 0.737 1.00 0.00 H
|
| 64 |
+
ATOM 63 CD2 TYR A 4 16.555 7.603 -0.128 1.00 0.00 C
|
| 65 |
+
ATOM 64 HD2 TYR A 4 15.983 8.067 0.676 1.00 0.00 H
|
| 66 |
+
ATOM 65 C TYR A 4 14.379 9.097 0.000 1.00 0.00 C
|
| 67 |
+
ATOM 66 O TYR A 4 13.616 10.060 0.000 1.00 0.00 O
|
| 68 |
+
ATOM 67 OXT TYR A 4 15.662 9.066 0.052 1.00 0.00 O
|
| 69 |
+
TER 68 TYR A 4
|
| 70 |
+
END
|
4AA-large/test/ADAS-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:bc4b7d57e19cb09116ad7532ef471d585df1470deb5125c4138c727d82204cca
|
| 3 |
+
size 774840073
|
4AA-large/test/ADAS-traj-state0.pdb
ADDED
|
@@ -0,0 +1,49 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH OPENMM 7.7, 2022-09-01
|
| 2 |
+
ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ALA A 1 2.492 1.313 0.836 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.647 1.445 -0.990 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
|
| 11 |
+
ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 12 |
+
ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 13 |
+
ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 14 |
+
ATOM 13 N ASP A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H ASP A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA ASP A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA ASP A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 CB ASP A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 19 |
+
ATOM 18 HB2 ASP A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 20 |
+
ATOM 19 HB3 ASP A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 21 |
+
ATOM 20 CG ASP A 2 9.715 3.149 -1.195 1.00 0.00 C
|
| 22 |
+
ATOM 21 OD1 ASP A 2 10.291 2.187 -0.620 1.00 0.00 O
|
| 23 |
+
ATOM 22 OD2 ASP A 2 10.291 4.128 -1.741 1.00 0.00 O
|
| 24 |
+
ATOM 23 C ASP A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 25 |
+
ATOM 24 O ASP A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 26 |
+
ATOM 25 N ALA A 3 9.517 5.386 0.000 1.00 0.00 N
|
| 27 |
+
ATOM 26 H ALA A 3 10.103 4.564 0.000 1.00 0.00 H
|
| 28 |
+
ATOM 27 CA ALA A 3 10.161 6.684 0.000 1.00 0.00 C
|
| 29 |
+
ATOM 28 HA ALA A 3 9.863 7.239 -0.890 1.00 0.00 H
|
| 30 |
+
ATOM 29 CB ALA A 3 9.768 7.492 1.232 1.00 0.00 C
|
| 31 |
+
ATOM 30 HB1 ALA A 3 10.068 6.954 2.131 1.00 0.00 H
|
| 32 |
+
ATOM 31 HB2 ALA A 3 10.266 8.462 1.206 1.00 0.00 H
|
| 33 |
+
ATOM 32 HB3 ALA A 3 8.688 7.640 1.241 1.00 0.00 H
|
| 34 |
+
ATOM 33 C ALA A 3 11.677 6.544 0.000 1.00 0.00 C
|
| 35 |
+
ATOM 34 O ALA A 3 12.200 5.432 0.000 1.00 0.00 O
|
| 36 |
+
ATOM 35 N SER A 4 12.382 7.677 0.000 1.00 0.00 N
|
| 37 |
+
ATOM 36 H SER A 4 11.906 8.568 0.000 1.00 0.00 H
|
| 38 |
+
ATOM 37 CA SER A 4 13.831 7.677 0.000 1.00 0.00 C
|
| 39 |
+
ATOM 38 HA SER A 4 14.195 7.163 0.890 1.00 0.00 H
|
| 40 |
+
ATOM 39 CB SER A 4 14.380 6.966 -1.232 1.00 0.00 C
|
| 41 |
+
ATOM 40 HB2 SER A 4 14.032 5.933 -1.241 1.00 0.00 H
|
| 42 |
+
ATOM 41 HB3 SER A 4 14.032 7.474 -2.131 1.00 0.00 H
|
| 43 |
+
ATOM 42 OG SER A 4 15.809 6.986 -1.197 1.00 0.00 O
|
| 44 |
+
ATOM 43 HG SER A 4 16.155 6.538 -1.973 1.00 0.00 H
|
| 45 |
+
ATOM 44 C SER A 4 14.379 9.097 0.000 1.00 0.00 C
|
| 46 |
+
ATOM 45 O SER A 4 13.616 10.060 0.000 1.00 0.00 O
|
| 47 |
+
ATOM 46 OXT SER A 4 15.666 9.046 0.051 1.00 0.00 O
|
| 48 |
+
TER 47 SER A 4
|
| 49 |
+
END
|
4AA-large/test/ADLL-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:b0e289a950407d2eea56dbee699c3a31179ed6f80ba47e63f4fd52b66963dbfb
|
| 3 |
+
size 1057381443
|
4AA-large/test/ADLL-traj-state0.pdb
ADDED
|
@@ -0,0 +1,66 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH OPENMM 7.7, 2022-09-01
|
| 2 |
+
ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ALA A 1 2.643 1.455 -0.989 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.494 1.309 0.837 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
|
| 11 |
+
ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 12 |
+
ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 13 |
+
ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 14 |
+
ATOM 13 N ASP A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H ASP A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA ASP A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA ASP A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 CB ASP A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 19 |
+
ATOM 18 HB2 ASP A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 20 |
+
ATOM 19 HB3 ASP A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 21 |
+
ATOM 20 CG ASP A 2 9.715 3.149 -1.195 1.00 0.00 C
|
| 22 |
+
ATOM 21 OD1 ASP A 2 10.291 2.187 -0.620 1.00 0.00 O
|
| 23 |
+
ATOM 22 OD2 ASP A 2 10.291 4.128 -1.741 1.00 0.00 O
|
| 24 |
+
ATOM 23 C ASP A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 25 |
+
ATOM 24 O ASP A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 26 |
+
ATOM 25 N LEU A 3 9.517 5.386 0.000 1.00 0.00 N
|
| 27 |
+
ATOM 26 H LEU A 3 10.103 4.564 0.000 1.00 0.00 H
|
| 28 |
+
ATOM 27 CA LEU A 3 10.161 6.684 0.000 1.00 0.00 C
|
| 29 |
+
ATOM 28 HA LEU A 3 9.863 7.239 -0.890 1.00 0.00 H
|
| 30 |
+
ATOM 29 CB LEU A 3 9.768 7.492 1.232 1.00 0.00 C
|
| 31 |
+
ATOM 30 HB2 LEU A 3 8.688 7.640 1.241 1.00 0.00 H
|
| 32 |
+
ATOM 31 HB3 LEU A 3 10.068 6.954 2.131 1.00 0.00 H
|
| 33 |
+
ATOM 32 CG LEU A 3 10.465 8.848 1.195 1.00 0.00 C
|
| 34 |
+
ATOM 33 HG LEU A 3 11.545 8.702 1.186 1.00 0.00 H
|
| 35 |
+
ATOM 34 CD1 LEU A 3 10.044 9.601 -0.063 1.00 0.00 C
|
| 36 |
+
ATOM 35 HD11 LEU A 3 8.964 9.749 -0.055 1.00 0.00 H
|
| 37 |
+
ATOM 36 HD12 LEU A 3 10.543 10.571 -0.090 1.00 0.00 H
|
| 38 |
+
ATOM 37 HD13 LEU A 3 10.325 9.024 -0.944 1.00 0.00 H
|
| 39 |
+
ATOM 38 CD2 LEU A 3 10.072 9.656 2.427 1.00 0.00 C
|
| 40 |
+
ATOM 39 HD21 LEU A 3 10.373 9.118 3.326 1.00 0.00 H
|
| 41 |
+
ATOM 40 HD22 LEU A 3 10.570 10.625 2.400 1.00 0.00 H
|
| 42 |
+
ATOM 41 HD23 LEU A 3 8.992 9.803 2.436 1.00 0.00 H
|
| 43 |
+
ATOM 42 C LEU A 3 11.677 6.544 0.000 1.00 0.00 C
|
| 44 |
+
ATOM 43 O LEU A 3 12.200 5.432 0.000 1.00 0.00 O
|
| 45 |
+
ATOM 44 N LEU A 4 12.382 7.677 0.000 1.00 0.00 N
|
| 46 |
+
ATOM 45 H LEU A 4 11.906 8.568 0.000 1.00 0.00 H
|
| 47 |
+
ATOM 46 CA LEU A 4 13.831 7.677 0.000 1.00 0.00 C
|
| 48 |
+
ATOM 47 HA LEU A 4 14.195 7.163 0.890 1.00 0.00 H
|
| 49 |
+
ATOM 48 CB LEU A 4 14.380 6.966 -1.232 1.00 0.00 C
|
| 50 |
+
ATOM 49 HB2 LEU A 4 14.032 5.933 -1.241 1.00 0.00 H
|
| 51 |
+
ATOM 50 HB3 LEU A 4 14.032 7.474 -2.131 1.00 0.00 H
|
| 52 |
+
ATOM 51 CG LEU A 4 15.904 6.987 -1.195 1.00 0.00 C
|
| 53 |
+
ATOM 52 HG LEU A 4 16.253 8.020 -1.186 1.00 0.00 H
|
| 54 |
+
ATOM 53 CD1 LEU A 4 16.392 6.276 0.063 1.00 0.00 C
|
| 55 |
+
ATOM 54 HD11 LEU A 4 16.044 5.243 0.055 1.00 0.00 H
|
| 56 |
+
ATOM 55 HD12 LEU A 4 17.482 6.291 0.090 1.00 0.00 H
|
| 57 |
+
ATOM 56 HD13 LEU A 4 16.000 6.784 0.944 1.00 0.00 H
|
| 58 |
+
ATOM 57 CD2 LEU A 4 16.453 6.276 -2.427 1.00 0.00 C
|
| 59 |
+
ATOM 58 HD21 LEU A 4 16.105 6.785 -3.326 1.00 0.00 H
|
| 60 |
+
ATOM 59 HD22 LEU A 4 17.543 6.291 -2.400 1.00 0.00 H
|
| 61 |
+
ATOM 60 HD23 LEU A 4 16.105 5.243 -2.436 1.00 0.00 H
|
| 62 |
+
ATOM 61 C LEU A 4 14.379 9.097 0.000 1.00 0.00 C
|
| 63 |
+
ATOM 62 O LEU A 4 13.616 10.060 0.000 1.00 0.00 O
|
| 64 |
+
ATOM 63 OXT LEU A 4 15.666 9.065 0.048 1.00 0.00 O
|
| 65 |
+
TER 64 LEU A 4
|
| 66 |
+
END
|
4AA-large/test/ADVF-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:96b1cd710a91f389986cea9e9ea34850fd966dfcb1e3465155ff426b851156d2
|
| 3 |
+
size 1024213585
|
4AA-large/test/ADVF-traj-state0.pdb
ADDED
|
@@ -0,0 +1,64 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH OPENMM 7.7, 2022-09-01
|
| 2 |
+
ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ALA A 1 2.494 1.314 0.838 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.633 1.451 -0.982 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
|
| 11 |
+
ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 12 |
+
ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 13 |
+
ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 14 |
+
ATOM 13 N ASP A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H ASP A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA ASP A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA ASP A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 CB ASP A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 19 |
+
ATOM 18 HB2 ASP A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 20 |
+
ATOM 19 HB3 ASP A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 21 |
+
ATOM 20 CG ASP A 2 9.715 3.149 -1.195 1.00 0.00 C
|
| 22 |
+
ATOM 21 OD1 ASP A 2 10.291 2.187 -0.620 1.00 0.00 O
|
| 23 |
+
ATOM 22 OD2 ASP A 2 10.291 4.128 -1.741 1.00 0.00 O
|
| 24 |
+
ATOM 23 C ASP A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 25 |
+
ATOM 24 O ASP A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 26 |
+
ATOM 25 N VAL A 3 9.517 5.386 0.000 1.00 0.00 N
|
| 27 |
+
ATOM 26 H VAL A 3 10.103 4.564 0.000 1.00 0.00 H
|
| 28 |
+
ATOM 27 CA VAL A 3 10.161 6.684 0.000 1.00 0.00 C
|
| 29 |
+
ATOM 28 HA VAL A 3 9.863 7.239 -0.890 1.00 0.00 H
|
| 30 |
+
ATOM 29 CB VAL A 3 9.768 7.492 1.232 1.00 0.00 C
|
| 31 |
+
ATOM 30 HB VAL A 3 8.688 7.640 1.241 1.00 0.00 H
|
| 32 |
+
ATOM 31 CG1 VAL A 3 10.189 6.739 2.490 1.00 0.00 C
|
| 33 |
+
ATOM 32 HG11 VAL A 3 11.269 6.592 2.481 1.00 0.00 H
|
| 34 |
+
ATOM 33 HG12 VAL A 3 9.908 7.316 3.371 1.00 0.00 H
|
| 35 |
+
ATOM 34 HG13 VAL A 3 9.691 5.770 2.517 1.00 0.00 H
|
| 36 |
+
ATOM 35 CG2 VAL A 3 10.465 8.848 1.195 1.00 0.00 C
|
| 37 |
+
ATOM 36 HG21 VAL A 3 10.165 9.387 0.296 1.00 0.00 H
|
| 38 |
+
ATOM 37 HG22 VAL A 3 10.185 9.426 2.075 1.00 0.00 H
|
| 39 |
+
ATOM 38 HG23 VAL A 3 11.545 8.702 1.186 1.00 0.00 H
|
| 40 |
+
ATOM 39 C VAL A 3 11.677 6.544 0.000 1.00 0.00 C
|
| 41 |
+
ATOM 40 O VAL A 3 12.200 5.432 0.000 1.00 0.00 O
|
| 42 |
+
ATOM 41 N PHE A 4 12.382 7.677 0.000 1.00 0.00 N
|
| 43 |
+
ATOM 42 H PHE A 4 11.906 8.568 0.000 1.00 0.00 H
|
| 44 |
+
ATOM 43 CA PHE A 4 13.831 7.677 0.000 1.00 0.00 C
|
| 45 |
+
ATOM 44 HA PHE A 4 14.195 7.163 0.890 1.00 0.00 H
|
| 46 |
+
ATOM 45 CB PHE A 4 14.380 6.966 -1.232 1.00 0.00 C
|
| 47 |
+
ATOM 46 HB2 PHE A 4 14.032 5.933 -1.241 1.00 0.00 H
|
| 48 |
+
ATOM 47 HB3 PHE A 4 14.032 7.474 -2.131 1.00 0.00 H
|
| 49 |
+
ATOM 48 CG PHE A 4 15.887 6.914 -1.321 1.00 0.00 C
|
| 50 |
+
ATOM 49 CD1 PHE A 4 16.502 6.286 -2.410 1.00 0.00 C
|
| 51 |
+
ATOM 50 HD1 PHE A 4 15.894 5.833 -3.193 1.00 0.00 H
|
| 52 |
+
ATOM 51 CE1 PHE A 4 17.899 6.238 -2.492 1.00 0.00 C
|
| 53 |
+
ATOM 52 HE1 PHE A 4 18.379 5.749 -3.340 1.00 0.00 H
|
| 54 |
+
ATOM 53 CZ PHE A 4 18.680 6.819 -1.486 1.00 0.00 C
|
| 55 |
+
ATOM 54 HZ PHE A 4 19.768 6.782 -1.550 1.00 0.00 H
|
| 56 |
+
ATOM 55 CE2 PHE A 4 18.064 7.448 -0.397 1.00 0.00 C
|
| 57 |
+
ATOM 56 HE2 PHE A 4 18.672 7.900 0.386 1.00 0.00 H
|
| 58 |
+
ATOM 57 CD2 PHE A 4 16.667 7.495 -0.315 1.00 0.00 C
|
| 59 |
+
ATOM 58 HD2 PHE A 4 16.188 7.985 0.533 1.00 0.00 H
|
| 60 |
+
ATOM 59 C PHE A 4 14.379 9.097 0.000 1.00 0.00 C
|
| 61 |
+
ATOM 60 O PHE A 4 13.616 10.060 0.000 1.00 0.00 O
|
| 62 |
+
ATOM 61 OXT PHE A 4 15.661 9.063 0.074 1.00 0.00 O
|
| 63 |
+
TER 62 PHE A 4
|
| 64 |
+
END
|
4AA-large/test/ADVK-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
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|
|
|
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|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:e2ae688b1b46e7fb6e351fecde50a3695baec30378b3d98799819532419ce9fc
|
| 3 |
+
size 1055761207
|
4AA-large/test/ADVK-traj-state0.pdb
ADDED
|
@@ -0,0 +1,66 @@
|
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|
|
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|
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|
|
|
|
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|
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|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH OPENMM 7.7, 2022-09-02
|
| 2 |
+
ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ALA A 1 2.497 1.305 0.839 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.639 1.450 -0.985 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
|
| 11 |
+
ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 12 |
+
ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 13 |
+
ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 14 |
+
ATOM 13 N ASP A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H ASP A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA ASP A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA ASP A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 CB ASP A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 19 |
+
ATOM 18 HB2 ASP A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 20 |
+
ATOM 19 HB3 ASP A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 21 |
+
ATOM 20 CG ASP A 2 9.715 3.149 -1.195 1.00 0.00 C
|
| 22 |
+
ATOM 21 OD1 ASP A 2 10.291 2.187 -0.620 1.00 0.00 O
|
| 23 |
+
ATOM 22 OD2 ASP A 2 10.291 4.128 -1.741 1.00 0.00 O
|
| 24 |
+
ATOM 23 C ASP A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 25 |
+
ATOM 24 O ASP A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 26 |
+
ATOM 25 N VAL A 3 9.517 5.386 0.000 1.00 0.00 N
|
| 27 |
+
ATOM 26 H VAL A 3 10.103 4.564 0.000 1.00 0.00 H
|
| 28 |
+
ATOM 27 CA VAL A 3 10.161 6.684 0.000 1.00 0.00 C
|
| 29 |
+
ATOM 28 HA VAL A 3 9.863 7.239 -0.890 1.00 0.00 H
|
| 30 |
+
ATOM 29 CB VAL A 3 9.768 7.492 1.232 1.00 0.00 C
|
| 31 |
+
ATOM 30 HB VAL A 3 8.688 7.640 1.241 1.00 0.00 H
|
| 32 |
+
ATOM 31 CG1 VAL A 3 10.189 6.739 2.490 1.00 0.00 C
|
| 33 |
+
ATOM 32 HG11 VAL A 3 11.269 6.592 2.481 1.00 0.00 H
|
| 34 |
+
ATOM 33 HG12 VAL A 3 9.908 7.316 3.371 1.00 0.00 H
|
| 35 |
+
ATOM 34 HG13 VAL A 3 9.691 5.770 2.517 1.00 0.00 H
|
| 36 |
+
ATOM 35 CG2 VAL A 3 10.465 8.848 1.195 1.00 0.00 C
|
| 37 |
+
ATOM 36 HG21 VAL A 3 10.165 9.387 0.296 1.00 0.00 H
|
| 38 |
+
ATOM 37 HG22 VAL A 3 10.185 9.426 2.075 1.00 0.00 H
|
| 39 |
+
ATOM 38 HG23 VAL A 3 11.545 8.702 1.186 1.00 0.00 H
|
| 40 |
+
ATOM 39 C VAL A 3 11.677 6.544 0.000 1.00 0.00 C
|
| 41 |
+
ATOM 40 O VAL A 3 12.200 5.432 0.000 1.00 0.00 O
|
| 42 |
+
ATOM 41 N LYS A 4 12.382 7.677 0.000 1.00 0.00 N
|
| 43 |
+
ATOM 42 H LYS A 4 11.906 8.568 0.000 1.00 0.00 H
|
| 44 |
+
ATOM 43 CA LYS A 4 13.831 7.677 0.000 1.00 0.00 C
|
| 45 |
+
ATOM 44 HA LYS A 4 14.195 7.163 0.890 1.00 0.00 H
|
| 46 |
+
ATOM 45 CB LYS A 4 14.380 6.966 -1.232 1.00 0.00 C
|
| 47 |
+
ATOM 46 HB2 LYS A 4 14.032 5.933 -1.241 1.00 0.00 H
|
| 48 |
+
ATOM 47 HB3 LYS A 4 14.032 7.474 -2.131 1.00 0.00 H
|
| 49 |
+
ATOM 48 CG LYS A 4 15.904 6.987 -1.195 1.00 0.00 C
|
| 50 |
+
ATOM 49 HG2 LYS A 4 16.253 8.020 -1.186 1.00 0.00 H
|
| 51 |
+
ATOM 50 HG3 LYS A 4 16.253 6.479 -0.296 1.00 0.00 H
|
| 52 |
+
ATOM 51 CD LYS A 4 16.453 6.276 -2.427 1.00 0.00 C
|
| 53 |
+
ATOM 52 HD2 LYS A 4 16.105 5.243 -2.436 1.00 0.00 H
|
| 54 |
+
ATOM 53 HD3 LYS A 4 16.105 6.785 -3.326 1.00 0.00 H
|
| 55 |
+
ATOM 54 CE LYS A 4 17.978 6.298 -2.389 1.00 0.00 C
|
| 56 |
+
ATOM 55 HE2 LYS A 4 18.327 7.330 -2.380 1.00 0.00 H
|
| 57 |
+
ATOM 56 HE3 LYS A 4 18.327 5.789 -1.491 1.00 0.00 H
|
| 58 |
+
ATOM 57 NZ LYS A 4 18.507 5.612 -3.577 1.00 0.00 N
|
| 59 |
+
ATOM 58 HZ1 LYS A 4 18.184 6.084 -4.410 1.00 0.00 H
|
| 60 |
+
ATOM 59 HZ2 LYS A 4 19.517 5.626 -3.552 1.00 0.00 H
|
| 61 |
+
ATOM 60 HZ3 LYS A 4 18.184 4.655 -3.585 1.00 0.00 H
|
| 62 |
+
ATOM 61 C LYS A 4 14.379 9.097 0.000 1.00 0.00 C
|
| 63 |
+
ATOM 62 O LYS A 4 13.616 10.060 0.000 1.00 0.00 O
|
| 64 |
+
ATOM 63 OXT LYS A 4 15.665 9.051 0.058 1.00 0.00 O
|
| 65 |
+
TER 64 LYS A 4
|
| 66 |
+
END
|
4AA-large/test/AEIS-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:a26440df376a48888c3c29d177986b9eee45c7a8f0b3de0a29de3b272faa6e7d
|
| 3 |
+
size 974554184
|
4AA-large/test/AEIS-traj-state0.pdb
ADDED
|
@@ -0,0 +1,61 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
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|
|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH OPENMM 7.7, 2022-09-01
|
| 2 |
+
ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ALA A 1 2.490 1.319 0.835 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.640 1.448 -0.986 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
|
| 11 |
+
ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 12 |
+
ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 13 |
+
ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 14 |
+
ATOM 13 N GLU A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H GLU A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA GLU A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA GLU A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 CB GLU A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 19 |
+
ATOM 18 HB2 GLU A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 20 |
+
ATOM 19 HB3 GLU A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 21 |
+
ATOM 20 CG GLU A 2 9.698 3.149 -1.195 1.00 0.00 C
|
| 22 |
+
ATOM 21 HG2 GLU A 2 10.047 4.181 -1.186 1.00 0.00 H
|
| 23 |
+
ATOM 22 HG3 GLU A 2 10.047 2.640 -0.296 1.00 0.00 H
|
| 24 |
+
ATOM 23 CD GLU A 2 10.248 2.436 -2.429 1.00 0.00 C
|
| 25 |
+
ATOM 24 OE1 GLU A 2 10.455 3.138 -3.454 1.00 0.00 O
|
| 26 |
+
ATOM 25 OE2 GLU A 2 10.455 1.197 -2.334 1.00 0.00 O
|
| 27 |
+
ATOM 26 C GLU A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 28 |
+
ATOM 27 O GLU A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 29 |
+
ATOM 28 N ILE A 3 9.517 5.386 0.000 1.00 0.00 N
|
| 30 |
+
ATOM 29 H ILE A 3 10.103 4.564 0.000 1.00 0.00 H
|
| 31 |
+
ATOM 30 CA ILE A 3 10.161 6.684 0.000 1.00 0.00 C
|
| 32 |
+
ATOM 31 HA ILE A 3 9.863 7.239 -0.890 1.00 0.00 H
|
| 33 |
+
ATOM 32 CB ILE A 3 9.743 7.459 1.245 1.00 0.00 C
|
| 34 |
+
ATOM 33 HB ILE A 3 8.661 7.591 1.246 1.00 0.00 H
|
| 35 |
+
ATOM 34 CG2 ILE A 3 10.161 6.684 2.490 1.00 0.00 C
|
| 36 |
+
ATOM 35 HG21 ILE A 3 11.243 6.553 2.491 1.00 0.00 H
|
| 37 |
+
ATOM 36 HG22 ILE A 3 9.863 7.238 3.381 1.00 0.00 H
|
| 38 |
+
ATOM 37 HG23 ILE A 3 9.677 5.708 2.491 1.00 0.00 H
|
| 39 |
+
ATOM 38 CG1 ILE A 3 10.421 8.825 1.245 1.00 0.00 C
|
| 40 |
+
ATOM 39 HG12 ILE A 3 11.503 8.694 1.245 1.00 0.00 H
|
| 41 |
+
ATOM 40 HG13 ILE A 3 10.123 9.380 0.355 1.00 0.00 H
|
| 42 |
+
ATOM 41 CD1 ILE A 3 10.003 9.600 2.490 1.00 0.00 C
|
| 43 |
+
ATOM 42 HD11 ILE A 3 10.302 9.047 3.381 1.00 0.00 H
|
| 44 |
+
ATOM 43 HD12 ILE A 3 10.488 10.577 2.491 1.00 0.00 H
|
| 45 |
+
ATOM 44 HD13 ILE A 3 8.921 9.732 2.491 1.00 0.00 H
|
| 46 |
+
ATOM 45 C ILE A 3 11.677 6.544 0.000 1.00 0.00 C
|
| 47 |
+
ATOM 46 O ILE A 3 12.200 5.432 0.000 1.00 0.00 O
|
| 48 |
+
ATOM 47 N SER A 4 12.382 7.677 0.000 1.00 0.00 N
|
| 49 |
+
ATOM 48 H SER A 4 11.906 8.568 0.000 1.00 0.00 H
|
| 50 |
+
ATOM 49 CA SER A 4 13.831 7.677 0.000 1.00 0.00 C
|
| 51 |
+
ATOM 50 HA SER A 4 14.195 7.163 0.890 1.00 0.00 H
|
| 52 |
+
ATOM 51 CB SER A 4 14.380 6.966 -1.232 1.00 0.00 C
|
| 53 |
+
ATOM 52 HB2 SER A 4 14.032 5.933 -1.241 1.00 0.00 H
|
| 54 |
+
ATOM 53 HB3 SER A 4 14.032 7.474 -2.131 1.00 0.00 H
|
| 55 |
+
ATOM 54 OG SER A 4 15.809 6.986 -1.197 1.00 0.00 O
|
| 56 |
+
ATOM 55 HG SER A 4 16.155 6.538 -1.973 1.00 0.00 H
|
| 57 |
+
ATOM 56 C SER A 4 14.379 9.097 0.000 1.00 0.00 C
|
| 58 |
+
ATOM 57 O SER A 4 13.616 10.060 0.000 1.00 0.00 O
|
| 59 |
+
ATOM 58 OXT SER A 4 15.666 9.049 0.042 1.00 0.00 O
|
| 60 |
+
TER 59 SER A 4
|
| 61 |
+
END
|
4AA-large/test/AEME-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:aa5ad640b76bfcc1a4c78705fefae56d95183ddedfdde9492b6c62ec7da391da
|
| 3 |
+
size 1007898825
|
4AA-large/test/AEME-traj-state0.pdb
ADDED
|
@@ -0,0 +1,63 @@
|
|
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|
|
|
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|
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|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH OPENMM 7.7, 2022-09-01
|
| 2 |
+
ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ALA A 1 2.496 1.307 0.838 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.642 1.448 -0.987 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
|
| 11 |
+
ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 12 |
+
ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 13 |
+
ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 14 |
+
ATOM 13 N GLU A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H GLU A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA GLU A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA GLU A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 CB GLU A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 19 |
+
ATOM 18 HB2 GLU A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 20 |
+
ATOM 19 HB3 GLU A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 21 |
+
ATOM 20 CG GLU A 2 9.698 3.149 -1.195 1.00 0.00 C
|
| 22 |
+
ATOM 21 HG2 GLU A 2 10.047 4.181 -1.186 1.00 0.00 H
|
| 23 |
+
ATOM 22 HG3 GLU A 2 10.047 2.640 -0.296 1.00 0.00 H
|
| 24 |
+
ATOM 23 CD GLU A 2 10.248 2.436 -2.429 1.00 0.00 C
|
| 25 |
+
ATOM 24 OE1 GLU A 2 10.455 3.138 -3.454 1.00 0.00 O
|
| 26 |
+
ATOM 25 OE2 GLU A 2 10.455 1.197 -2.334 1.00 0.00 O
|
| 27 |
+
ATOM 26 C GLU A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 28 |
+
ATOM 27 O GLU A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 29 |
+
ATOM 28 N MET A 3 9.517 5.386 0.000 1.00 0.00 N
|
| 30 |
+
ATOM 29 H MET A 3 10.103 4.564 0.000 1.00 0.00 H
|
| 31 |
+
ATOM 30 CA MET A 3 10.161 6.684 0.000 1.00 0.00 C
|
| 32 |
+
ATOM 31 HA MET A 3 9.863 7.239 -0.890 1.00 0.00 H
|
| 33 |
+
ATOM 32 CB MET A 3 9.768 7.492 1.232 1.00 0.00 C
|
| 34 |
+
ATOM 33 HB2 MET A 3 8.688 7.640 1.241 1.00 0.00 H
|
| 35 |
+
ATOM 34 HB3 MET A 3 10.068 6.954 2.131 1.00 0.00 H
|
| 36 |
+
ATOM 35 CG MET A 3 10.465 8.848 1.195 1.00 0.00 C
|
| 37 |
+
ATOM 36 HG2 MET A 3 11.545 8.702 1.186 1.00 0.00 H
|
| 38 |
+
ATOM 37 HG3 MET A 3 10.165 9.387 0.296 1.00 0.00 H
|
| 39 |
+
ATOM 38 SD MET A 3 10.008 9.820 2.652 1.00 0.00 S
|
| 40 |
+
ATOM 39 CE MET A 3 10.944 11.302 2.341 1.00 0.00 C
|
| 41 |
+
ATOM 40 HE1 MET A 3 10.625 11.743 1.397 1.00 0.00 H
|
| 42 |
+
ATOM 41 HE2 MET A 3 10.777 12.014 3.149 1.00 0.00 H
|
| 43 |
+
ATOM 42 HE3 MET A 3 12.005 11.057 2.287 1.00 0.00 H
|
| 44 |
+
ATOM 43 C MET A 3 11.677 6.544 0.000 1.00 0.00 C
|
| 45 |
+
ATOM 44 O MET A 3 12.200 5.432 0.000 1.00 0.00 O
|
| 46 |
+
ATOM 45 N GLU A 4 12.382 7.677 0.000 1.00 0.00 N
|
| 47 |
+
ATOM 46 H GLU A 4 11.906 8.568 0.000 1.00 0.00 H
|
| 48 |
+
ATOM 47 CA GLU A 4 13.831 7.677 0.000 1.00 0.00 C
|
| 49 |
+
ATOM 48 HA GLU A 4 14.195 7.163 0.890 1.00 0.00 H
|
| 50 |
+
ATOM 49 CB GLU A 4 14.380 6.966 -1.232 1.00 0.00 C
|
| 51 |
+
ATOM 50 HB2 GLU A 4 14.032 5.933 -1.241 1.00 0.00 H
|
| 52 |
+
ATOM 51 HB3 GLU A 4 14.032 7.474 -2.131 1.00 0.00 H
|
| 53 |
+
ATOM 52 CG GLU A 4 15.889 6.987 -1.195 1.00 0.00 C
|
| 54 |
+
ATOM 53 HG2 GLU A 4 16.238 8.020 -1.186 1.00 0.00 H
|
| 55 |
+
ATOM 54 HG3 GLU A 4 16.238 6.479 -0.296 1.00 0.00 H
|
| 56 |
+
ATOM 55 CD GLU A 4 16.439 6.275 -2.429 1.00 0.00 C
|
| 57 |
+
ATOM 56 OE1 GLU A 4 16.646 6.977 -3.454 1.00 0.00 O
|
| 58 |
+
ATOM 57 OE2 GLU A 4 16.646 5.036 -2.334 1.00 0.00 O
|
| 59 |
+
ATOM 58 C GLU A 4 14.379 9.097 0.000 1.00 0.00 C
|
| 60 |
+
ATOM 59 O GLU A 4 13.616 10.060 0.000 1.00 0.00 O
|
| 61 |
+
ATOM 60 OXT GLU A 4 15.666 9.052 0.048 1.00 0.00 O
|
| 62 |
+
TER 61 GLU A 4
|
| 63 |
+
END
|
4AA-large/test/AEVI-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:84d396bb0a9aa6bc74debae47f738db95539ad15d1cedb69e289d49c9ef6dd30
|
| 3 |
+
size 1057902640
|
4AA-large/test/AEVI-traj-state0.pdb
ADDED
|
@@ -0,0 +1,66 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH OPENMM 7.7, 2022-09-01
|
| 2 |
+
ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ALA A 1 2.477 1.310 0.820 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.661 1.447 -1.000 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
|
| 11 |
+
ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 12 |
+
ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 13 |
+
ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 14 |
+
ATOM 13 N GLU A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H GLU A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA GLU A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA GLU A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 CB GLU A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 19 |
+
ATOM 18 HB2 GLU A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 20 |
+
ATOM 19 HB3 GLU A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 21 |
+
ATOM 20 CG GLU A 2 9.698 3.149 -1.195 1.00 0.00 C
|
| 22 |
+
ATOM 21 HG2 GLU A 2 10.047 4.181 -1.186 1.00 0.00 H
|
| 23 |
+
ATOM 22 HG3 GLU A 2 10.047 2.640 -0.296 1.00 0.00 H
|
| 24 |
+
ATOM 23 CD GLU A 2 10.248 2.436 -2.429 1.00 0.00 C
|
| 25 |
+
ATOM 24 OE1 GLU A 2 10.455 3.138 -3.454 1.00 0.00 O
|
| 26 |
+
ATOM 25 OE2 GLU A 2 10.455 1.197 -2.334 1.00 0.00 O
|
| 27 |
+
ATOM 26 C GLU A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 28 |
+
ATOM 27 O GLU A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 29 |
+
ATOM 28 N VAL A 3 9.517 5.386 0.000 1.00 0.00 N
|
| 30 |
+
ATOM 29 H VAL A 3 10.103 4.564 0.000 1.00 0.00 H
|
| 31 |
+
ATOM 30 CA VAL A 3 10.161 6.684 0.000 1.00 0.00 C
|
| 32 |
+
ATOM 31 HA VAL A 3 9.863 7.239 -0.890 1.00 0.00 H
|
| 33 |
+
ATOM 32 CB VAL A 3 9.768 7.492 1.232 1.00 0.00 C
|
| 34 |
+
ATOM 33 HB VAL A 3 8.688 7.640 1.241 1.00 0.00 H
|
| 35 |
+
ATOM 34 CG1 VAL A 3 10.189 6.739 2.490 1.00 0.00 C
|
| 36 |
+
ATOM 35 HG11 VAL A 3 11.269 6.592 2.481 1.00 0.00 H
|
| 37 |
+
ATOM 36 HG12 VAL A 3 9.908 7.316 3.371 1.00 0.00 H
|
| 38 |
+
ATOM 37 HG13 VAL A 3 9.691 5.770 2.517 1.00 0.00 H
|
| 39 |
+
ATOM 38 CG2 VAL A 3 10.465 8.848 1.195 1.00 0.00 C
|
| 40 |
+
ATOM 39 HG21 VAL A 3 10.165 9.387 0.296 1.00 0.00 H
|
| 41 |
+
ATOM 40 HG22 VAL A 3 10.185 9.426 2.075 1.00 0.00 H
|
| 42 |
+
ATOM 41 HG23 VAL A 3 11.545 8.702 1.186 1.00 0.00 H
|
| 43 |
+
ATOM 42 C VAL A 3 11.677 6.544 0.000 1.00 0.00 C
|
| 44 |
+
ATOM 43 O VAL A 3 12.200 5.432 0.000 1.00 0.00 O
|
| 45 |
+
ATOM 44 N ILE A 4 12.382 7.677 0.000 1.00 0.00 N
|
| 46 |
+
ATOM 45 H ILE A 4 11.906 8.568 0.000 1.00 0.00 H
|
| 47 |
+
ATOM 46 CA ILE A 4 13.831 7.677 0.000 1.00 0.00 C
|
| 48 |
+
ATOM 47 HA ILE A 4 14.195 7.163 0.890 1.00 0.00 H
|
| 49 |
+
ATOM 48 CB ILE A 4 14.339 6.958 -1.245 1.00 0.00 C
|
| 50 |
+
ATOM 49 HB ILE A 4 13.976 5.931 -1.246 1.00 0.00 H
|
| 51 |
+
ATOM 50 CG2 ILE A 4 13.831 7.677 -2.490 1.00 0.00 C
|
| 52 |
+
ATOM 51 HG21 ILE A 4 14.194 8.705 -2.491 1.00 0.00 H
|
| 53 |
+
ATOM 52 HG22 ILE A 4 14.194 7.164 -3.381 1.00 0.00 H
|
| 54 |
+
ATOM 53 HG23 ILE A 4 12.741 7.677 -2.491 1.00 0.00 H
|
| 55 |
+
ATOM 54 CG1 ILE A 4 15.864 6.958 -1.245 1.00 0.00 C
|
| 56 |
+
ATOM 55 HG12 ILE A 4 16.228 7.986 -1.245 1.00 0.00 H
|
| 57 |
+
ATOM 56 HG13 ILE A 4 16.228 6.445 -0.355 1.00 0.00 H
|
| 58 |
+
ATOM 57 CD1 ILE A 4 16.373 6.239 -2.490 1.00 0.00 C
|
| 59 |
+
ATOM 58 HD11 ILE A 4 16.010 6.753 -3.381 1.00 0.00 H
|
| 60 |
+
ATOM 59 HD12 ILE A 4 17.463 6.239 -2.491 1.00 0.00 H
|
| 61 |
+
ATOM 60 HD13 ILE A 4 16.010 5.212 -2.491 1.00 0.00 H
|
| 62 |
+
ATOM 61 C ILE A 4 14.379 9.097 0.000 1.00 0.00 C
|
| 63 |
+
ATOM 62 O ILE A 4 13.616 10.060 0.000 1.00 0.00 O
|
| 64 |
+
ATOM 63 OXT ILE A 4 15.666 9.052 0.064 1.00 0.00 O
|
| 65 |
+
TER 64 ILE A 4
|
| 66 |
+
END
|
4AA-large/test/AFIA-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:735c3492cfe18eee3e80f91adeb4d11dddefaf40a1846cf1500544617d8f8c23
|
| 3 |
+
size 1041267379
|
4AA-large/test/AFIA-traj-state0.pdb
ADDED
|
@@ -0,0 +1,65 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH OPENMM 7.7, 2022-09-01
|
| 2 |
+
ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ALA A 1 2.496 1.310 0.839 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.642 1.448 -0.987 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
|
| 11 |
+
ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 12 |
+
ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 13 |
+
ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 14 |
+
ATOM 13 N PHE A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H PHE A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA PHE A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA PHE A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 CB PHE A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 19 |
+
ATOM 18 HB2 PHE A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 20 |
+
ATOM 19 HB3 PHE A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 21 |
+
ATOM 20 CG PHE A 2 9.696 3.076 -1.321 1.00 0.00 C
|
| 22 |
+
ATOM 21 CD1 PHE A 2 10.311 2.447 -2.410 1.00 0.00 C
|
| 23 |
+
ATOM 22 HD1 PHE A 2 9.703 1.995 -3.193 1.00 0.00 H
|
| 24 |
+
ATOM 23 CE1 PHE A 2 11.708 2.400 -2.492 1.00 0.00 C
|
| 25 |
+
ATOM 24 HE1 PHE A 2 12.188 1.910 -3.340 1.00 0.00 H
|
| 26 |
+
ATOM 25 CZ PHE A 2 12.489 2.981 -1.486 1.00 0.00 C
|
| 27 |
+
ATOM 26 HZ PHE A 2 13.576 2.944 -1.550 1.00 0.00 H
|
| 28 |
+
ATOM 27 CE2 PHE A 2 11.873 3.609 -0.397 1.00 0.00 C
|
| 29 |
+
ATOM 28 HE2 PHE A 2 12.481 4.062 0.386 1.00 0.00 H
|
| 30 |
+
ATOM 29 CD2 PHE A 2 10.476 3.657 -0.315 1.00 0.00 C
|
| 31 |
+
ATOM 30 HD2 PHE A 2 9.997 4.146 0.533 1.00 0.00 H
|
| 32 |
+
ATOM 31 C PHE A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 33 |
+
ATOM 32 O PHE A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 34 |
+
ATOM 33 N ILE A 3 9.517 5.386 0.000 1.00 0.00 N
|
| 35 |
+
ATOM 34 H ILE A 3 10.103 4.564 0.000 1.00 0.00 H
|
| 36 |
+
ATOM 35 CA ILE A 3 10.161 6.684 0.000 1.00 0.00 C
|
| 37 |
+
ATOM 36 HA ILE A 3 9.863 7.239 -0.890 1.00 0.00 H
|
| 38 |
+
ATOM 37 CB ILE A 3 9.743 7.459 1.245 1.00 0.00 C
|
| 39 |
+
ATOM 38 HB ILE A 3 8.661 7.591 1.246 1.00 0.00 H
|
| 40 |
+
ATOM 39 CG2 ILE A 3 10.161 6.684 2.490 1.00 0.00 C
|
| 41 |
+
ATOM 40 HG21 ILE A 3 11.243 6.553 2.491 1.00 0.00 H
|
| 42 |
+
ATOM 41 HG22 ILE A 3 9.863 7.238 3.381 1.00 0.00 H
|
| 43 |
+
ATOM 42 HG23 ILE A 3 9.677 5.708 2.491 1.00 0.00 H
|
| 44 |
+
ATOM 43 CG1 ILE A 3 10.421 8.825 1.245 1.00 0.00 C
|
| 45 |
+
ATOM 44 HG12 ILE A 3 11.503 8.694 1.245 1.00 0.00 H
|
| 46 |
+
ATOM 45 HG13 ILE A 3 10.123 9.380 0.355 1.00 0.00 H
|
| 47 |
+
ATOM 46 CD1 ILE A 3 10.003 9.600 2.490 1.00 0.00 C
|
| 48 |
+
ATOM 47 HD11 ILE A 3 10.302 9.047 3.381 1.00 0.00 H
|
| 49 |
+
ATOM 48 HD12 ILE A 3 10.488 10.577 2.491 1.00 0.00 H
|
| 50 |
+
ATOM 49 HD13 ILE A 3 8.921 9.732 2.491 1.00 0.00 H
|
| 51 |
+
ATOM 50 C ILE A 3 11.677 6.544 0.000 1.00 0.00 C
|
| 52 |
+
ATOM 51 O ILE A 3 12.200 5.432 0.000 1.00 0.00 O
|
| 53 |
+
ATOM 52 N ALA A 4 12.382 7.677 0.000 1.00 0.00 N
|
| 54 |
+
ATOM 53 H ALA A 4 11.906 8.568 0.000 1.00 0.00 H
|
| 55 |
+
ATOM 54 CA ALA A 4 13.831 7.677 0.000 1.00 0.00 C
|
| 56 |
+
ATOM 55 HA ALA A 4 14.195 7.163 0.890 1.00 0.00 H
|
| 57 |
+
ATOM 56 CB ALA A 4 14.380 6.966 -1.232 1.00 0.00 C
|
| 58 |
+
ATOM 57 HB1 ALA A 4 14.032 7.474 -2.131 1.00 0.00 H
|
| 59 |
+
ATOM 58 HB2 ALA A 4 15.470 6.981 -1.206 1.00 0.00 H
|
| 60 |
+
ATOM 59 HB3 ALA A 4 14.032 5.933 -1.241 1.00 0.00 H
|
| 61 |
+
ATOM 60 C ALA A 4 14.379 9.097 0.000 1.00 0.00 C
|
| 62 |
+
ATOM 61 O ALA A 4 13.616 10.060 0.000 1.00 0.00 O
|
| 63 |
+
ATOM 62 OXT ALA A 4 15.666 9.034 0.012 1.00 0.00 O
|
| 64 |
+
TER 63 ALA A 4
|
| 65 |
+
END
|
4AA-large/test/AFPN-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:bab64ec1731294125f077d144291974c0d653efa104347f2bb36496786728c96
|
| 3 |
+
size 1025001082
|
4AA-large/test/AFPN-traj-state0.pdb
ADDED
|
@@ -0,0 +1,64 @@
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH OPENMM 7.7, 2022-09-01
|
| 2 |
+
ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ALA A 1 2.644 1.447 -0.988 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.499 1.305 0.840 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
|
| 11 |
+
ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 12 |
+
ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 13 |
+
ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 14 |
+
ATOM 13 N PHE A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H PHE A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA PHE A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA PHE A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 CB PHE A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 19 |
+
ATOM 18 HB2 PHE A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 20 |
+
ATOM 19 HB3 PHE A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 21 |
+
ATOM 20 CG PHE A 2 9.696 3.076 -1.321 1.00 0.00 C
|
| 22 |
+
ATOM 21 CD1 PHE A 2 10.311 2.447 -2.410 1.00 0.00 C
|
| 23 |
+
ATOM 22 HD1 PHE A 2 9.703 1.995 -3.193 1.00 0.00 H
|
| 24 |
+
ATOM 23 CE1 PHE A 2 11.708 2.400 -2.492 1.00 0.00 C
|
| 25 |
+
ATOM 24 HE1 PHE A 2 12.188 1.910 -3.340 1.00 0.00 H
|
| 26 |
+
ATOM 25 CZ PHE A 2 12.489 2.981 -1.486 1.00 0.00 C
|
| 27 |
+
ATOM 26 HZ PHE A 2 13.576 2.944 -1.550 1.00 0.00 H
|
| 28 |
+
ATOM 27 CE2 PHE A 2 11.873 3.609 -0.397 1.00 0.00 C
|
| 29 |
+
ATOM 28 HE2 PHE A 2 12.481 4.062 0.386 1.00 0.00 H
|
| 30 |
+
ATOM 29 CD2 PHE A 2 10.476 3.657 -0.315 1.00 0.00 C
|
| 31 |
+
ATOM 30 HD2 PHE A 2 9.997 4.146 0.533 1.00 0.00 H
|
| 32 |
+
ATOM 31 C PHE A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 33 |
+
ATOM 32 O PHE A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 34 |
+
ATOM 33 N PRO A 3 9.517 5.386 0.000 1.00 0.00 N
|
| 35 |
+
ATOM 34 CD PRO A 3 10.402 4.228 0.000 1.00 0.00 C
|
| 36 |
+
ATOM 35 HD2 PRO A 3 10.493 3.840 -1.014 1.00 0.00 H
|
| 37 |
+
ATOM 36 HD3 PRO A 3 9.990 3.455 0.649 1.00 0.00 H
|
| 38 |
+
ATOM 37 CG PRO A 3 11.694 4.785 0.522 1.00 0.00 C
|
| 39 |
+
ATOM 38 HG2 PRO A 3 12.522 4.324 -0.016 1.00 0.00 H
|
| 40 |
+
ATOM 39 HG3 PRO A 3 11.789 4.570 1.586 1.00 0.00 H
|
| 41 |
+
ATOM 40 CB PRO A 3 11.636 6.273 0.276 1.00 0.00 C
|
| 42 |
+
ATOM 41 HB2 PRO A 3 12.257 6.519 -0.586 1.00 0.00 H
|
| 43 |
+
ATOM 42 HB3 PRO A 3 12.011 6.797 1.155 1.00 0.00 H
|
| 44 |
+
ATOM 43 CA PRO A 3 10.162 6.686 0.000 1.00 0.00 C
|
| 45 |
+
ATOM 44 HA PRO A 3 9.895 7.263 0.886 1.00 0.00 H
|
| 46 |
+
ATOM 45 C PRO A 3 9.798 7.477 -1.248 1.00 0.00 C
|
| 47 |
+
ATOM 46 O PRO A 3 8.999 7.022 -2.064 1.00 0.00 O
|
| 48 |
+
ATOM 47 N ASN A 4 10.388 8.665 -1.396 1.00 0.00 N
|
| 49 |
+
ATOM 48 H ASN A 4 11.039 8.997 -0.698 1.00 0.00 H
|
| 50 |
+
ATOM 49 CA ASN A 4 10.125 9.514 -2.541 1.00 0.00 C
|
| 51 |
+
ATOM 50 HA ASN A 4 10.403 8.988 -3.455 1.00 0.00 H
|
| 52 |
+
ATOM 51 CB ASN A 4 8.648 9.884 -2.622 1.00 0.00 C
|
| 53 |
+
ATOM 52 HB2 ASN A 4 8.050 8.978 -2.716 1.00 0.00 H
|
| 54 |
+
ATOM 53 HB3 ASN A 4 8.357 10.419 -1.718 1.00 0.00 H
|
| 55 |
+
ATOM 54 CG ASN A 4 8.372 10.775 -3.825 1.00 0.00 C
|
| 56 |
+
ATOM 55 OD1 ASN A 4 9.284 11.104 -4.581 1.00 0.00 O
|
| 57 |
+
ATOM 56 ND2 ASN A 4 7.108 11.166 -4.002 1.00 0.00 N
|
| 58 |
+
ATOM 57 HD21 ASN A 4 6.870 11.759 -4.784 1.00 0.00 H
|
| 59 |
+
ATOM 58 HD22 ASN A 4 6.395 10.868 -3.351 1.00 0.00 H
|
| 60 |
+
ATOM 59 C ASN A 4 10.925 10.806 -2.461 1.00 0.00 C
|
| 61 |
+
ATOM 60 O ASN A 4 11.674 11.018 -1.510 1.00 0.00 O
|
| 62 |
+
ATOM 61 OXT ASN A 4 10.723 11.504 -3.523 1.00 0.00 O
|
| 63 |
+
TER 62 ASN A 4
|
| 64 |
+
END
|
4AA-large/test/AGAK-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:8d640288f394072d242522515d4c0399f065eed97b4d851d04f5a5febdb55138
|
| 3 |
+
size 872550397
|
4AA-large/test/AGAK-traj-state0.pdb
ADDED
|
@@ -0,0 +1,55 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH OPENMM 7.7, 2022-09-02
|
| 2 |
+
ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ALA A 1 2.649 1.450 -0.992 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.491 1.309 0.834 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
|
| 11 |
+
ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 12 |
+
ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 13 |
+
ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 14 |
+
ATOM 13 N GLY A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H GLY A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA GLY A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA2 GLY A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 HA3 GLY A 2 8.004 3.325 -0.890 1.00 0.00 H
|
| 19 |
+
ATOM 18 C GLY A 2 8.171 5.265 0.000 1.00 0.00 C
|
| 20 |
+
ATOM 19 O GLY A 2 7.395 6.219 0.000 1.00 0.00 O
|
| 21 |
+
ATOM 20 N ALA A 3 9.498 5.409 0.000 1.00 0.00 N
|
| 22 |
+
ATOM 21 H ALA A 3 10.094 4.594 0.000 1.00 0.00 H
|
| 23 |
+
ATOM 22 CA ALA A 3 10.126 6.715 0.000 1.00 0.00 C
|
| 24 |
+
ATOM 23 HA ALA A 3 9.821 7.266 -0.890 1.00 0.00 H
|
| 25 |
+
ATOM 24 CB ALA A 3 9.723 7.518 1.232 1.00 0.00 C
|
| 26 |
+
ATOM 25 HB1 ALA A 3 10.030 6.984 2.131 1.00 0.00 H
|
| 27 |
+
ATOM 26 HB2 ALA A 3 10.209 8.493 1.206 1.00 0.00 H
|
| 28 |
+
ATOM 27 HB3 ALA A 3 8.641 7.652 1.241 1.00 0.00 H
|
| 29 |
+
ATOM 28 C ALA A 3 11.643 6.593 0.000 1.00 0.00 C
|
| 30 |
+
ATOM 29 O ALA A 3 12.180 5.487 0.000 1.00 0.00 O
|
| 31 |
+
ATOM 30 N LYS A 4 12.335 7.735 0.000 1.00 0.00 N
|
| 32 |
+
ATOM 31 H LYS A 4 11.848 8.620 0.000 1.00 0.00 H
|
| 33 |
+
ATOM 32 CA LYS A 4 13.784 7.753 0.000 1.00 0.00 C
|
| 34 |
+
ATOM 33 HA LYS A 4 14.154 7.243 0.890 1.00 0.00 H
|
| 35 |
+
ATOM 34 CB LYS A 4 14.341 7.048 -1.232 1.00 0.00 C
|
| 36 |
+
ATOM 35 HB2 LYS A 4 14.006 6.011 -1.241 1.00 0.00 H
|
| 37 |
+
ATOM 36 HB3 LYS A 4 13.987 7.552 -2.131 1.00 0.00 H
|
| 38 |
+
ATOM 37 CG LYS A 4 15.865 7.088 -1.195 1.00 0.00 C
|
| 39 |
+
ATOM 38 HG2 LYS A 4 16.202 8.125 -1.186 1.00 0.00 H
|
| 40 |
+
ATOM 39 HG3 LYS A 4 16.221 6.584 -0.296 1.00 0.00 H
|
| 41 |
+
ATOM 40 CD LYS A 4 16.423 6.384 -2.427 1.00 0.00 C
|
| 42 |
+
ATOM 41 HD2 LYS A 4 16.087 5.347 -2.436 1.00 0.00 H
|
| 43 |
+
ATOM 42 HD3 LYS A 4 16.068 6.888 -3.326 1.00 0.00 H
|
| 44 |
+
ATOM 43 CE LYS A 4 17.947 6.424 -2.389 1.00 0.00 C
|
| 45 |
+
ATOM 44 HE2 LYS A 4 18.283 7.461 -2.380 1.00 0.00 H
|
| 46 |
+
ATOM 45 HE3 LYS A 4 18.302 5.920 -1.491 1.00 0.00 H
|
| 47 |
+
ATOM 46 NZ LYS A 4 18.484 5.745 -3.577 1.00 0.00 N
|
| 48 |
+
ATOM 47 HZ1 LYS A 4 18.156 6.212 -4.410 1.00 0.00 H
|
| 49 |
+
ATOM 48 HZ2 LYS A 4 19.494 5.771 -3.552 1.00 0.00 H
|
| 50 |
+
ATOM 49 HZ3 LYS A 4 18.173 4.784 -3.585 1.00 0.00 H
|
| 51 |
+
ATOM 50 C LYS A 4 14.314 9.179 0.000 1.00 0.00 C
|
| 52 |
+
ATOM 51 O LYS A 4 13.539 10.133 0.000 1.00 0.00 O
|
| 53 |
+
ATOM 52 OXT LYS A 4 15.601 9.146 0.063 1.00 0.00 O
|
| 54 |
+
TER 53 LYS A 4
|
| 55 |
+
END
|
4AA-large/test/AHSH-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:7aa6546011c522f921e327e9fb2b88a17a4a1dce6b71d3ec3486113aceea2640
|
| 3 |
+
size 972616060
|
4AA-large/test/AHSH-traj-state0.pdb
ADDED
|
@@ -0,0 +1,61 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH OPENMM 7.7, 2022-09-02
|
| 2 |
+
ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ALA A 1 2.493 1.312 0.837 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.644 1.445 -0.988 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
|
| 11 |
+
ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 12 |
+
ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 13 |
+
ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 14 |
+
ATOM 13 N HIS A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H HIS A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA HIS A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA HIS A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 CB HIS A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 19 |
+
ATOM 18 HB2 HIS A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 20 |
+
ATOM 19 HB3 HIS A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 21 |
+
ATOM 20 CG HIS A 2 9.696 3.076 -1.321 1.00 0.00 C
|
| 22 |
+
ATOM 21 ND1 HIS A 2 10.350 2.463 -2.383 1.00 0.00 N
|
| 23 |
+
ATOM 22 CE1 HIS A 2 11.650 2.579 -2.183 1.00 0.00 C
|
| 24 |
+
ATOM 23 HE1 HIS A 2 12.352 2.162 -2.905 1.00 0.00 H
|
| 25 |
+
ATOM 24 NE2 HIS A 2 11.852 3.226 -1.062 1.00 0.00 N
|
| 26 |
+
ATOM 25 HE2 HIS A 2 12.759 3.448 -0.677 1.00 0.00 H
|
| 27 |
+
ATOM 26 CD2 HIS A 2 10.662 3.554 -0.492 1.00 0.00 C
|
| 28 |
+
ATOM 27 HD2 HIS A 2 10.641 4.099 0.451 1.00 0.00 H
|
| 29 |
+
ATOM 28 C HIS A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 30 |
+
ATOM 29 O HIS A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 31 |
+
ATOM 30 N SER A 3 9.517 5.386 0.000 1.00 0.00 N
|
| 32 |
+
ATOM 31 H SER A 3 10.103 4.564 0.000 1.00 0.00 H
|
| 33 |
+
ATOM 32 CA SER A 3 10.161 6.684 0.000 1.00 0.00 C
|
| 34 |
+
ATOM 33 HA SER A 3 9.863 7.239 -0.890 1.00 0.00 H
|
| 35 |
+
ATOM 34 CB SER A 3 9.768 7.492 1.232 1.00 0.00 C
|
| 36 |
+
ATOM 35 HB2 SER A 3 8.688 7.640 1.241 1.00 0.00 H
|
| 37 |
+
ATOM 36 HB3 SER A 3 10.068 6.954 2.131 1.00 0.00 H
|
| 38 |
+
ATOM 37 OG SER A 3 10.422 8.764 1.197 1.00 0.00 O
|
| 39 |
+
ATOM 38 HG SER A 3 10.174 9.272 1.973 1.00 0.00 H
|
| 40 |
+
ATOM 39 C SER A 3 11.677 6.544 0.000 1.00 0.00 C
|
| 41 |
+
ATOM 40 O SER A 3 12.200 5.432 0.000 1.00 0.00 O
|
| 42 |
+
ATOM 41 N HIS A 4 12.382 7.677 0.000 1.00 0.00 N
|
| 43 |
+
ATOM 42 H HIS A 4 11.906 8.568 0.000 1.00 0.00 H
|
| 44 |
+
ATOM 43 CA HIS A 4 13.831 7.677 0.000 1.00 0.00 C
|
| 45 |
+
ATOM 44 HA HIS A 4 14.195 7.163 0.890 1.00 0.00 H
|
| 46 |
+
ATOM 45 CB HIS A 4 14.380 6.966 -1.232 1.00 0.00 C
|
| 47 |
+
ATOM 46 HB2 HIS A 4 14.032 5.933 -1.241 1.00 0.00 H
|
| 48 |
+
ATOM 47 HB3 HIS A 4 14.032 7.474 -2.131 1.00 0.00 H
|
| 49 |
+
ATOM 48 CG HIS A 4 15.887 6.914 -1.321 1.00 0.00 C
|
| 50 |
+
ATOM 49 ND1 HIS A 4 16.541 6.301 -2.383 1.00 0.00 N
|
| 51 |
+
ATOM 50 CE1 HIS A 4 17.841 6.417 -2.183 1.00 0.00 C
|
| 52 |
+
ATOM 51 HE1 HIS A 4 18.543 6.000 -2.905 1.00 0.00 H
|
| 53 |
+
ATOM 52 NE2 HIS A 4 18.043 7.064 -1.062 1.00 0.00 N
|
| 54 |
+
ATOM 53 HE2 HIS A 4 18.950 7.286 -0.677 1.00 0.00 H
|
| 55 |
+
ATOM 54 CD2 HIS A 4 16.853 7.393 -0.492 1.00 0.00 C
|
| 56 |
+
ATOM 55 HD2 HIS A 4 16.832 7.938 0.451 1.00 0.00 H
|
| 57 |
+
ATOM 56 C HIS A 4 14.379 9.097 0.000 1.00 0.00 C
|
| 58 |
+
ATOM 57 O HIS A 4 13.616 10.060 0.000 1.00 0.00 O
|
| 59 |
+
ATOM 58 OXT HIS A 4 15.662 9.061 0.080 1.00 0.00 O
|
| 60 |
+
TER 59 HIS A 4
|
| 61 |
+
END
|
4AA-large/test/AIAV-traj-state0.pdb
ADDED
|
@@ -0,0 +1,61 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH OPENMM 7.7, 2022-09-02
|
| 2 |
+
ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ALA A 1 2.637 1.447 -0.984 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.497 1.310 0.840 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
|
| 11 |
+
ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 12 |
+
ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 13 |
+
ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 14 |
+
ATOM 13 N ILE A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H ILE A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA ILE A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA ILE A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 CB ILE A 2 8.148 3.120 -1.245 1.00 0.00 C
|
| 19 |
+
ATOM 18 HB ILE A 2 7.785 2.092 -1.246 1.00 0.00 H
|
| 20 |
+
ATOM 19 CG2 ILE A 2 7.640 3.839 -2.490 1.00 0.00 C
|
| 21 |
+
ATOM 20 HG21 ILE A 2 8.003 4.866 -2.491 1.00 0.00 H
|
| 22 |
+
ATOM 21 HG22 ILE A 2 8.003 3.325 -3.381 1.00 0.00 H
|
| 23 |
+
ATOM 22 HG23 ILE A 2 6.550 3.839 -2.491 1.00 0.00 H
|
| 24 |
+
ATOM 23 CG1 ILE A 2 9.673 3.120 -1.245 1.00 0.00 C
|
| 25 |
+
ATOM 24 HG12 ILE A 2 10.037 4.147 -1.245 1.00 0.00 H
|
| 26 |
+
ATOM 25 HG13 ILE A 2 10.037 2.606 -0.355 1.00 0.00 H
|
| 27 |
+
ATOM 26 CD1 ILE A 2 10.182 2.401 -2.490 1.00 0.00 C
|
| 28 |
+
ATOM 27 HD11 ILE A 2 9.819 2.914 -3.381 1.00 0.00 H
|
| 29 |
+
ATOM 28 HD12 ILE A 2 11.272 2.401 -2.491 1.00 0.00 H
|
| 30 |
+
ATOM 29 HD13 ILE A 2 9.819 1.373 -2.491 1.00 0.00 H
|
| 31 |
+
ATOM 30 C ILE A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 32 |
+
ATOM 31 O ILE A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 33 |
+
ATOM 32 N ALA A 3 9.517 5.386 0.000 1.00 0.00 N
|
| 34 |
+
ATOM 33 H ALA A 3 10.103 4.564 0.000 1.00 0.00 H
|
| 35 |
+
ATOM 34 CA ALA A 3 10.161 6.684 0.000 1.00 0.00 C
|
| 36 |
+
ATOM 35 HA ALA A 3 9.863 7.239 -0.890 1.00 0.00 H
|
| 37 |
+
ATOM 36 CB ALA A 3 9.768 7.492 1.232 1.00 0.00 C
|
| 38 |
+
ATOM 37 HB1 ALA A 3 10.068 6.954 2.131 1.00 0.00 H
|
| 39 |
+
ATOM 38 HB2 ALA A 3 10.266 8.462 1.206 1.00 0.00 H
|
| 40 |
+
ATOM 39 HB3 ALA A 3 8.688 7.640 1.241 1.00 0.00 H
|
| 41 |
+
ATOM 40 C ALA A 3 11.677 6.544 0.000 1.00 0.00 C
|
| 42 |
+
ATOM 41 O ALA A 3 12.200 5.432 0.000 1.00 0.00 O
|
| 43 |
+
ATOM 42 N VAL A 4 12.382 7.677 0.000 1.00 0.00 N
|
| 44 |
+
ATOM 43 H VAL A 4 11.906 8.568 0.000 1.00 0.00 H
|
| 45 |
+
ATOM 44 CA VAL A 4 13.831 7.677 0.000 1.00 0.00 C
|
| 46 |
+
ATOM 45 HA VAL A 4 14.195 7.163 0.890 1.00 0.00 H
|
| 47 |
+
ATOM 46 CB VAL A 4 14.380 6.966 -1.232 1.00 0.00 C
|
| 48 |
+
ATOM 47 HB VAL A 4 14.032 5.933 -1.241 1.00 0.00 H
|
| 49 |
+
ATOM 48 CG1 VAL A 4 13.892 7.678 -2.490 1.00 0.00 C
|
| 50 |
+
ATOM 49 HG11 VAL A 4 14.241 8.710 -2.481 1.00 0.00 H
|
| 51 |
+
ATOM 50 HG12 VAL A 4 14.284 7.170 -3.371 1.00 0.00 H
|
| 52 |
+
ATOM 51 HG13 VAL A 4 12.803 7.662 -2.517 1.00 0.00 H
|
| 53 |
+
ATOM 52 CG2 VAL A 4 15.904 6.987 -1.195 1.00 0.00 C
|
| 54 |
+
ATOM 53 HG21 VAL A 4 16.253 6.479 -0.296 1.00 0.00 H
|
| 55 |
+
ATOM 54 HG22 VAL A 4 16.297 6.479 -2.075 1.00 0.00 H
|
| 56 |
+
ATOM 55 HG23 VAL A 4 16.253 8.020 -1.186 1.00 0.00 H
|
| 57 |
+
ATOM 56 C VAL A 4 14.379 9.097 0.000 1.00 0.00 C
|
| 58 |
+
ATOM 57 O VAL A 4 13.616 10.060 0.000 1.00 0.00 O
|
| 59 |
+
ATOM 58 OXT VAL A 4 15.666 9.048 0.063 1.00 0.00 O
|
| 60 |
+
TER 59 VAL A 4
|
| 61 |
+
END
|
4AA-large/test/AKFR-traj-state0.pdb
ADDED
|
@@ -0,0 +1,82 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH OPENMM 7.7, 2022-09-02
|
| 2 |
+
ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ALA A 1 2.645 1.439 -0.989 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.501 1.309 0.844 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
|
| 11 |
+
ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 12 |
+
ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 13 |
+
ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 14 |
+
ATOM 13 N LYS A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H LYS A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA LYS A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA LYS A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 CB LYS A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 19 |
+
ATOM 18 HB2 LYS A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 20 |
+
ATOM 19 HB3 LYS A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 21 |
+
ATOM 20 CG LYS A 2 9.713 3.149 -1.195 1.00 0.00 C
|
| 22 |
+
ATOM 21 HG2 LYS A 2 10.062 4.181 -1.186 1.00 0.00 H
|
| 23 |
+
ATOM 22 HG3 LYS A 2 10.062 2.640 -0.296 1.00 0.00 H
|
| 24 |
+
ATOM 23 CD LYS A 2 10.262 2.438 -2.427 1.00 0.00 C
|
| 25 |
+
ATOM 24 HD2 LYS A 2 9.914 1.405 -2.436 1.00 0.00 H
|
| 26 |
+
ATOM 25 HD3 LYS A 2 9.914 2.946 -3.326 1.00 0.00 H
|
| 27 |
+
ATOM 26 CE LYS A 2 11.787 2.459 -2.389 1.00 0.00 C
|
| 28 |
+
ATOM 27 HE2 LYS A 2 12.136 3.492 -2.380 1.00 0.00 H
|
| 29 |
+
ATOM 28 HE3 LYS A 2 12.136 1.951 -1.491 1.00 0.00 H
|
| 30 |
+
ATOM 29 NZ LYS A 2 12.316 1.773 -3.577 1.00 0.00 N
|
| 31 |
+
ATOM 30 HZ1 LYS A 2 11.993 2.245 -4.410 1.00 0.00 H
|
| 32 |
+
ATOM 31 HZ2 LYS A 2 13.326 1.788 -3.552 1.00 0.00 H
|
| 33 |
+
ATOM 32 HZ3 LYS A 2 11.993 0.817 -3.585 1.00 0.00 H
|
| 34 |
+
ATOM 33 C LYS A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 35 |
+
ATOM 34 O LYS A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 36 |
+
ATOM 35 N PHE A 3 9.517 5.386 0.000 1.00 0.00 N
|
| 37 |
+
ATOM 36 H PHE A 3 10.103 4.564 0.000 1.00 0.00 H
|
| 38 |
+
ATOM 37 CA PHE A 3 10.161 6.684 0.000 1.00 0.00 C
|
| 39 |
+
ATOM 38 HA PHE A 3 9.863 7.239 -0.890 1.00 0.00 H
|
| 40 |
+
ATOM 39 CB PHE A 3 9.768 7.492 1.232 1.00 0.00 C
|
| 41 |
+
ATOM 40 HB2 PHE A 3 8.688 7.640 1.241 1.00 0.00 H
|
| 42 |
+
ATOM 41 HB3 PHE A 3 10.068 6.954 2.131 1.00 0.00 H
|
| 43 |
+
ATOM 42 CG PHE A 3 10.392 8.865 1.321 1.00 0.00 C
|
| 44 |
+
ATOM 43 CD1 PHE A 3 10.103 9.696 2.410 1.00 0.00 C
|
| 45 |
+
ATOM 44 HD1 PHE A 3 9.427 9.352 3.193 1.00 0.00 H
|
| 46 |
+
ATOM 45 CE1 PHE A 3 10.681 10.968 2.492 1.00 0.00 C
|
| 47 |
+
ATOM 46 HE1 PHE A 3 10.456 11.615 3.340 1.00 0.00 H
|
| 48 |
+
ATOM 47 CZ PHE A 3 11.549 11.409 1.486 1.00 0.00 C
|
| 49 |
+
ATOM 48 HZ PHE A 3 11.999 12.400 1.550 1.00 0.00 H
|
| 50 |
+
ATOM 49 CE2 PHE A 3 11.838 10.578 0.397 1.00 0.00 C
|
| 51 |
+
ATOM 50 HE2 PHE A 3 12.513 10.921 -0.386 1.00 0.00 H
|
| 52 |
+
ATOM 51 CD2 PHE A 3 11.259 9.306 0.315 1.00 0.00 C
|
| 53 |
+
ATOM 52 HD2 PHE A 3 11.485 8.659 -0.533 1.00 0.00 H
|
| 54 |
+
ATOM 53 C PHE A 3 11.677 6.544 0.000 1.00 0.00 C
|
| 55 |
+
ATOM 54 O PHE A 3 12.200 5.432 0.000 1.00 0.00 O
|
| 56 |
+
ATOM 55 N ARG A 4 12.382 7.677 0.000 1.00 0.00 N
|
| 57 |
+
ATOM 56 H ARG A 4 11.906 8.568 0.000 1.00 0.00 H
|
| 58 |
+
ATOM 57 CA ARG A 4 13.831 7.677 0.000 1.00 0.00 C
|
| 59 |
+
ATOM 58 HA ARG A 4 14.195 7.163 0.890 1.00 0.00 H
|
| 60 |
+
ATOM 59 CB ARG A 4 14.380 6.966 -1.232 1.00 0.00 C
|
| 61 |
+
ATOM 60 HB2 ARG A 4 14.032 5.933 -1.241 1.00 0.00 H
|
| 62 |
+
ATOM 61 HB3 ARG A 4 14.032 7.474 -2.131 1.00 0.00 H
|
| 63 |
+
ATOM 62 CG ARG A 4 15.904 6.987 -1.195 1.00 0.00 C
|
| 64 |
+
ATOM 63 HG2 ARG A 4 16.253 8.020 -1.186 1.00 0.00 H
|
| 65 |
+
ATOM 64 HG3 ARG A 4 16.253 6.479 -0.296 1.00 0.00 H
|
| 66 |
+
ATOM 65 CD ARG A 4 16.453 6.276 -2.427 1.00 0.00 C
|
| 67 |
+
ATOM 66 HD2 ARG A 4 16.105 5.243 -2.436 1.00 0.00 H
|
| 68 |
+
ATOM 67 HD3 ARG A 4 16.105 6.785 -3.326 1.00 0.00 H
|
| 69 |
+
ATOM 68 NE ARG A 4 17.933 6.277 -2.425 1.00 0.00 N
|
| 70 |
+
ATOM 69 HE ARG A 4 18.414 6.722 -1.655 1.00 0.00 H
|
| 71 |
+
ATOM 70 CZ ARG A 4 18.660 5.720 -3.389 1.00 0.00 C
|
| 72 |
+
ATOM 71 NH1 ARG A 4 18.100 5.117 -4.434 1.00 0.00 N
|
| 73 |
+
ATOM 72 HH11 ARG A 4 17.093 5.074 -4.509 1.00 0.00 H
|
| 74 |
+
ATOM 73 HH12 ARG A 4 18.683 4.705 -5.148 1.00 0.00 H
|
| 75 |
+
ATOM 74 NH2 ARG A 4 19.984 5.779 -3.287 1.00 0.00 N
|
| 76 |
+
ATOM 75 HH21 ARG A 4 20.406 6.238 -2.492 1.00 0.00 H
|
| 77 |
+
ATOM 76 HH22 ARG A 4 20.562 5.365 -4.004 1.00 0.00 H
|
| 78 |
+
ATOM 77 C ARG A 4 14.379 9.097 0.000 1.00 0.00 C
|
| 79 |
+
ATOM 78 O ARG A 4 13.616 10.060 0.000 1.00 0.00 O
|
| 80 |
+
ATOM 79 OXT ARG A 4 15.667 9.053 0.026 1.00 0.00 O
|
| 81 |
+
TER 80 ARG A 4
|
| 82 |
+
END
|
4AA-large/test/AKSL-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:6c2605b134009fc8bd2c3457933e0f05b61d636dd5dfb7bb9d0aa95b12ac6d84
|
| 3 |
+
size 1091310327
|
4AA-large/test/AKSL-traj-state0.pdb
ADDED
|
@@ -0,0 +1,68 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
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|
|
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|
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|
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|
|
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|
|
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|
|
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|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH OPENMM 7.7, 2022-09-01
|
| 2 |
+
ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ALA A 1 2.494 1.318 0.840 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.639 1.446 -0.985 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
|
| 11 |
+
ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 12 |
+
ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 13 |
+
ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 14 |
+
ATOM 13 N LYS A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H LYS A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA LYS A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA LYS A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 CB LYS A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 19 |
+
ATOM 18 HB2 LYS A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 20 |
+
ATOM 19 HB3 LYS A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 21 |
+
ATOM 20 CG LYS A 2 9.713 3.149 -1.195 1.00 0.00 C
|
| 22 |
+
ATOM 21 HG2 LYS A 2 10.062 4.181 -1.186 1.00 0.00 H
|
| 23 |
+
ATOM 22 HG3 LYS A 2 10.062 2.640 -0.296 1.00 0.00 H
|
| 24 |
+
ATOM 23 CD LYS A 2 10.262 2.438 -2.427 1.00 0.00 C
|
| 25 |
+
ATOM 24 HD2 LYS A 2 9.914 1.405 -2.436 1.00 0.00 H
|
| 26 |
+
ATOM 25 HD3 LYS A 2 9.914 2.946 -3.326 1.00 0.00 H
|
| 27 |
+
ATOM 26 CE LYS A 2 11.787 2.459 -2.389 1.00 0.00 C
|
| 28 |
+
ATOM 27 HE2 LYS A 2 12.136 3.492 -2.380 1.00 0.00 H
|
| 29 |
+
ATOM 28 HE3 LYS A 2 12.136 1.951 -1.491 1.00 0.00 H
|
| 30 |
+
ATOM 29 NZ LYS A 2 12.316 1.773 -3.577 1.00 0.00 N
|
| 31 |
+
ATOM 30 HZ1 LYS A 2 11.993 2.245 -4.410 1.00 0.00 H
|
| 32 |
+
ATOM 31 HZ2 LYS A 2 13.326 1.788 -3.552 1.00 0.00 H
|
| 33 |
+
ATOM 32 HZ3 LYS A 2 11.993 0.817 -3.585 1.00 0.00 H
|
| 34 |
+
ATOM 33 C LYS A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 35 |
+
ATOM 34 O LYS A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 36 |
+
ATOM 35 N SER A 3 9.517 5.386 0.000 1.00 0.00 N
|
| 37 |
+
ATOM 36 H SER A 3 10.103 4.564 0.000 1.00 0.00 H
|
| 38 |
+
ATOM 37 CA SER A 3 10.161 6.684 0.000 1.00 0.00 C
|
| 39 |
+
ATOM 38 HA SER A 3 9.863 7.239 -0.890 1.00 0.00 H
|
| 40 |
+
ATOM 39 CB SER A 3 9.768 7.492 1.232 1.00 0.00 C
|
| 41 |
+
ATOM 40 HB2 SER A 3 8.688 7.640 1.241 1.00 0.00 H
|
| 42 |
+
ATOM 41 HB3 SER A 3 10.068 6.954 2.131 1.00 0.00 H
|
| 43 |
+
ATOM 42 OG SER A 3 10.422 8.764 1.197 1.00 0.00 O
|
| 44 |
+
ATOM 43 HG SER A 3 10.174 9.272 1.973 1.00 0.00 H
|
| 45 |
+
ATOM 44 C SER A 3 11.677 6.544 0.000 1.00 0.00 C
|
| 46 |
+
ATOM 45 O SER A 3 12.200 5.432 0.000 1.00 0.00 O
|
| 47 |
+
ATOM 46 N LEU A 4 12.382 7.677 0.000 1.00 0.00 N
|
| 48 |
+
ATOM 47 H LEU A 4 11.906 8.568 0.000 1.00 0.00 H
|
| 49 |
+
ATOM 48 CA LEU A 4 13.831 7.677 0.000 1.00 0.00 C
|
| 50 |
+
ATOM 49 HA LEU A 4 14.195 7.163 0.890 1.00 0.00 H
|
| 51 |
+
ATOM 50 CB LEU A 4 14.380 6.966 -1.232 1.00 0.00 C
|
| 52 |
+
ATOM 51 HB2 LEU A 4 14.032 5.933 -1.241 1.00 0.00 H
|
| 53 |
+
ATOM 52 HB3 LEU A 4 14.032 7.474 -2.131 1.00 0.00 H
|
| 54 |
+
ATOM 53 CG LEU A 4 15.904 6.987 -1.195 1.00 0.00 C
|
| 55 |
+
ATOM 54 HG LEU A 4 16.253 8.020 -1.186 1.00 0.00 H
|
| 56 |
+
ATOM 55 CD1 LEU A 4 16.392 6.276 0.063 1.00 0.00 C
|
| 57 |
+
ATOM 56 HD11 LEU A 4 16.044 5.243 0.055 1.00 0.00 H
|
| 58 |
+
ATOM 57 HD12 LEU A 4 17.482 6.291 0.090 1.00 0.00 H
|
| 59 |
+
ATOM 58 HD13 LEU A 4 16.000 6.784 0.944 1.00 0.00 H
|
| 60 |
+
ATOM 59 CD2 LEU A 4 16.453 6.276 -2.427 1.00 0.00 C
|
| 61 |
+
ATOM 60 HD21 LEU A 4 16.105 6.785 -3.326 1.00 0.00 H
|
| 62 |
+
ATOM 61 HD22 LEU A 4 17.543 6.291 -2.400 1.00 0.00 H
|
| 63 |
+
ATOM 62 HD23 LEU A 4 16.105 5.243 -2.436 1.00 0.00 H
|
| 64 |
+
ATOM 63 C LEU A 4 14.379 9.097 0.000 1.00 0.00 C
|
| 65 |
+
ATOM 64 O LEU A 4 13.616 10.060 0.000 1.00 0.00 O
|
| 66 |
+
ATOM 65 OXT LEU A 4 15.666 9.061 0.053 1.00 0.00 O
|
| 67 |
+
TER 66 LEU A 4
|
| 68 |
+
END
|
4AA-large/test/ALEF-traj-state0.pdb
ADDED
|
@@ -0,0 +1,70 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH OPENMM 7.7, 2022-09-01
|
| 2 |
+
ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ALA A 1 2.489 1.311 0.832 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.647 1.450 -0.990 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
|
| 11 |
+
ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 12 |
+
ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 13 |
+
ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 14 |
+
ATOM 13 N LEU A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H LEU A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA LEU A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA LEU A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 CB LEU A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 19 |
+
ATOM 18 HB2 LEU A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 20 |
+
ATOM 19 HB3 LEU A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 21 |
+
ATOM 20 CG LEU A 2 9.713 3.149 -1.195 1.00 0.00 C
|
| 22 |
+
ATOM 21 HG LEU A 2 10.062 4.181 -1.186 1.00 0.00 H
|
| 23 |
+
ATOM 22 CD1 LEU A 2 10.201 2.437 0.063 1.00 0.00 C
|
| 24 |
+
ATOM 23 HD11 LEU A 2 9.853 1.404 0.055 1.00 0.00 H
|
| 25 |
+
ATOM 24 HD12 LEU A 2 11.291 2.452 0.090 1.00 0.00 H
|
| 26 |
+
ATOM 25 HD13 LEU A 2 9.809 2.945 0.944 1.00 0.00 H
|
| 27 |
+
ATOM 26 CD2 LEU A 2 10.262 2.438 -2.427 1.00 0.00 C
|
| 28 |
+
ATOM 27 HD21 LEU A 2 9.914 2.946 -3.326 1.00 0.00 H
|
| 29 |
+
ATOM 28 HD22 LEU A 2 11.352 2.453 -2.400 1.00 0.00 H
|
| 30 |
+
ATOM 29 HD23 LEU A 2 9.914 1.405 -2.436 1.00 0.00 H
|
| 31 |
+
ATOM 30 C LEU A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 32 |
+
ATOM 31 O LEU A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 33 |
+
ATOM 32 N GLU A 3 9.517 5.386 0.000 1.00 0.00 N
|
| 34 |
+
ATOM 33 H GLU A 3 10.103 4.564 0.000 1.00 0.00 H
|
| 35 |
+
ATOM 34 CA GLU A 3 10.161 6.684 0.000 1.00 0.00 C
|
| 36 |
+
ATOM 35 HA GLU A 3 9.863 7.239 -0.890 1.00 0.00 H
|
| 37 |
+
ATOM 36 CB GLU A 3 9.768 7.492 1.232 1.00 0.00 C
|
| 38 |
+
ATOM 37 HB2 GLU A 3 8.688 7.640 1.241 1.00 0.00 H
|
| 39 |
+
ATOM 38 HB3 GLU A 3 10.068 6.954 2.131 1.00 0.00 H
|
| 40 |
+
ATOM 39 CG GLU A 3 10.458 8.835 1.195 1.00 0.00 C
|
| 41 |
+
ATOM 40 HG2 GLU A 3 11.538 8.688 1.186 1.00 0.00 H
|
| 42 |
+
ATOM 41 HG3 GLU A 3 10.158 9.374 0.296 1.00 0.00 H
|
| 43 |
+
ATOM 42 CD GLU A 3 10.065 9.644 2.429 1.00 0.00 C
|
| 44 |
+
ATOM 43 OE1 GLU A 3 10.786 9.518 3.454 1.00 0.00 O
|
| 45 |
+
ATOM 44 OE2 GLU A 3 9.047 10.381 2.334 1.00 0.00 O
|
| 46 |
+
ATOM 45 C GLU A 3 11.677 6.544 0.000 1.00 0.00 C
|
| 47 |
+
ATOM 46 O GLU A 3 12.200 5.432 0.000 1.00 0.00 O
|
| 48 |
+
ATOM 47 N PHE A 4 12.382 7.677 0.000 1.00 0.00 N
|
| 49 |
+
ATOM 48 H PHE A 4 11.906 8.568 0.000 1.00 0.00 H
|
| 50 |
+
ATOM 49 CA PHE A 4 13.831 7.677 0.000 1.00 0.00 C
|
| 51 |
+
ATOM 50 HA PHE A 4 14.195 7.163 0.890 1.00 0.00 H
|
| 52 |
+
ATOM 51 CB PHE A 4 14.380 6.966 -1.232 1.00 0.00 C
|
| 53 |
+
ATOM 52 HB2 PHE A 4 14.032 5.933 -1.241 1.00 0.00 H
|
| 54 |
+
ATOM 53 HB3 PHE A 4 14.032 7.474 -2.131 1.00 0.00 H
|
| 55 |
+
ATOM 54 CG PHE A 4 15.887 6.914 -1.321 1.00 0.00 C
|
| 56 |
+
ATOM 55 CD1 PHE A 4 16.502 6.286 -2.410 1.00 0.00 C
|
| 57 |
+
ATOM 56 HD1 PHE A 4 15.894 5.833 -3.193 1.00 0.00 H
|
| 58 |
+
ATOM 57 CE1 PHE A 4 17.899 6.238 -2.492 1.00 0.00 C
|
| 59 |
+
ATOM 58 HE1 PHE A 4 18.379 5.749 -3.340 1.00 0.00 H
|
| 60 |
+
ATOM 59 CZ PHE A 4 18.680 6.819 -1.486 1.00 0.00 C
|
| 61 |
+
ATOM 60 HZ PHE A 4 19.768 6.782 -1.550 1.00 0.00 H
|
| 62 |
+
ATOM 61 CE2 PHE A 4 18.064 7.448 -0.397 1.00 0.00 C
|
| 63 |
+
ATOM 62 HE2 PHE A 4 18.672 7.900 0.386 1.00 0.00 H
|
| 64 |
+
ATOM 63 CD2 PHE A 4 16.667 7.495 -0.315 1.00 0.00 C
|
| 65 |
+
ATOM 64 HD2 PHE A 4 16.188 7.985 0.533 1.00 0.00 H
|
| 66 |
+
ATOM 65 C PHE A 4 14.379 9.097 0.000 1.00 0.00 C
|
| 67 |
+
ATOM 66 O PHE A 4 13.616 10.060 0.000 1.00 0.00 O
|
| 68 |
+
ATOM 67 OXT PHE A 4 15.661 9.064 0.065 1.00 0.00 O
|
| 69 |
+
TER 68 PHE A 4
|
| 70 |
+
END
|
4AA-large/test/ALTQ-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:215facffe6ffc91d8a3a4e53101d47d1ea4ccdaafe0bb322d9b39f50350525dc
|
| 3 |
+
size 1057756454
|
4AA-large/test/ALTQ-traj-state0.pdb
ADDED
|
@@ -0,0 +1,66 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH OPENMM 7.7, 2022-09-01
|
| 2 |
+
ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ALA A 1 2.644 1.447 -0.989 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.490 1.314 0.834 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
|
| 11 |
+
ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 12 |
+
ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 13 |
+
ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 14 |
+
ATOM 13 N LEU A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H LEU A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA LEU A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA LEU A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 CB LEU A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 19 |
+
ATOM 18 HB2 LEU A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 20 |
+
ATOM 19 HB3 LEU A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 21 |
+
ATOM 20 CG LEU A 2 9.713 3.149 -1.195 1.00 0.00 C
|
| 22 |
+
ATOM 21 HG LEU A 2 10.062 4.181 -1.186 1.00 0.00 H
|
| 23 |
+
ATOM 22 CD1 LEU A 2 10.201 2.437 0.063 1.00 0.00 C
|
| 24 |
+
ATOM 23 HD11 LEU A 2 9.853 1.404 0.055 1.00 0.00 H
|
| 25 |
+
ATOM 24 HD12 LEU A 2 11.291 2.452 0.090 1.00 0.00 H
|
| 26 |
+
ATOM 25 HD13 LEU A 2 9.809 2.945 0.944 1.00 0.00 H
|
| 27 |
+
ATOM 26 CD2 LEU A 2 10.262 2.438 -2.427 1.00 0.00 C
|
| 28 |
+
ATOM 27 HD21 LEU A 2 9.914 2.946 -3.326 1.00 0.00 H
|
| 29 |
+
ATOM 28 HD22 LEU A 2 11.352 2.453 -2.400 1.00 0.00 H
|
| 30 |
+
ATOM 29 HD23 LEU A 2 9.914 1.405 -2.436 1.00 0.00 H
|
| 31 |
+
ATOM 30 C LEU A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 32 |
+
ATOM 31 O LEU A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 33 |
+
ATOM 32 N THR A 3 9.517 5.386 0.000 1.00 0.00 N
|
| 34 |
+
ATOM 33 H THR A 3 10.103 4.564 0.000 1.00 0.00 H
|
| 35 |
+
ATOM 34 CA THR A 3 10.161 6.684 0.000 1.00 0.00 C
|
| 36 |
+
ATOM 35 HA THR A 3 9.863 7.239 -0.890 1.00 0.00 H
|
| 37 |
+
ATOM 36 CB THR A 3 9.768 7.492 1.232 1.00 0.00 C
|
| 38 |
+
ATOM 37 HB THR A 3 10.266 8.462 1.206 1.00 0.00 H
|
| 39 |
+
ATOM 38 CG2 THR A 3 8.257 7.698 1.244 1.00 0.00 C
|
| 40 |
+
ATOM 39 HG21 THR A 3 7.758 6.729 1.271 1.00 0.00 H
|
| 41 |
+
ATOM 40 HG22 THR A 3 7.975 8.276 2.125 1.00 0.00 H
|
| 42 |
+
ATOM 41 HG23 THR A 3 7.956 8.236 0.346 1.00 0.00 H
|
| 43 |
+
ATOM 42 OG1 THR A 3 10.163 6.786 2.411 1.00 0.00 O
|
| 44 |
+
ATOM 43 HG1 THR A 3 9.915 7.295 3.187 1.00 0.00 H
|
| 45 |
+
ATOM 44 C THR A 3 11.677 6.544 0.000 1.00 0.00 C
|
| 46 |
+
ATOM 45 O THR A 3 12.200 5.432 0.000 1.00 0.00 O
|
| 47 |
+
ATOM 46 N GLN A 4 12.382 7.677 0.000 1.00 0.00 N
|
| 48 |
+
ATOM 47 H GLN A 4 11.906 8.568 0.000 1.00 0.00 H
|
| 49 |
+
ATOM 48 CA GLN A 4 13.831 7.677 0.000 1.00 0.00 C
|
| 50 |
+
ATOM 49 HA GLN A 4 14.195 7.163 0.890 1.00 0.00 H
|
| 51 |
+
ATOM 50 CB GLN A 4 14.380 6.966 -1.232 1.00 0.00 C
|
| 52 |
+
ATOM 51 HB2 GLN A 4 14.032 5.933 -1.241 1.00 0.00 H
|
| 53 |
+
ATOM 52 HB3 GLN A 4 14.032 7.474 -2.131 1.00 0.00 H
|
| 54 |
+
ATOM 53 CG GLN A 4 15.904 6.987 -1.195 1.00 0.00 C
|
| 55 |
+
ATOM 54 HG2 GLN A 4 16.253 8.020 -1.186 1.00 0.00 H
|
| 56 |
+
ATOM 55 HG3 GLN A 4 16.253 6.479 -0.296 1.00 0.00 H
|
| 57 |
+
ATOM 56 CD GLN A 4 16.492 6.286 -2.410 1.00 0.00 C
|
| 58 |
+
ATOM 57 OE1 GLN A 4 15.757 5.793 -3.263 1.00 0.00 O
|
| 59 |
+
ATOM 58 NE2 GLN A 4 17.824 6.241 -2.488 1.00 0.00 N
|
| 60 |
+
ATOM 59 HE21 GLN A 4 18.266 5.786 -3.275 1.00 0.00 H
|
| 61 |
+
ATOM 60 HE22 GLN A 4 18.384 6.661 -1.760 1.00 0.00 H
|
| 62 |
+
ATOM 61 C GLN A 4 14.379 9.097 0.000 1.00 0.00 C
|
| 63 |
+
ATOM 62 O GLN A 4 13.616 10.060 0.000 1.00 0.00 O
|
| 64 |
+
ATOM 63 OXT GLN A 4 15.665 9.050 0.065 1.00 0.00 O
|
| 65 |
+
TER 64 GLN A 4
|
| 66 |
+
END
|
4AA-large/test/ALTV-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:c68eae31f0fbc17a108ebf56ddf202540281891a46f05643410edbfe052dcbea
|
| 3 |
+
size 1038781865
|
4AA-large/test/ALTV-traj-state0.pdb
ADDED
|
@@ -0,0 +1,65 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH OPENMM 7.7, 2022-09-02
|
| 2 |
+
ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ALA A 1 2.493 1.315 0.838 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.641 1.441 -0.986 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
|
| 11 |
+
ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 12 |
+
ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 13 |
+
ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 14 |
+
ATOM 13 N LEU A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H LEU A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA LEU A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA LEU A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 CB LEU A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 19 |
+
ATOM 18 HB2 LEU A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 20 |
+
ATOM 19 HB3 LEU A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 21 |
+
ATOM 20 CG LEU A 2 9.713 3.149 -1.195 1.00 0.00 C
|
| 22 |
+
ATOM 21 HG LEU A 2 10.062 4.181 -1.186 1.00 0.00 H
|
| 23 |
+
ATOM 22 CD1 LEU A 2 10.201 2.437 0.063 1.00 0.00 C
|
| 24 |
+
ATOM 23 HD11 LEU A 2 9.853 1.404 0.055 1.00 0.00 H
|
| 25 |
+
ATOM 24 HD12 LEU A 2 11.291 2.452 0.090 1.00 0.00 H
|
| 26 |
+
ATOM 25 HD13 LEU A 2 9.809 2.945 0.944 1.00 0.00 H
|
| 27 |
+
ATOM 26 CD2 LEU A 2 10.262 2.438 -2.427 1.00 0.00 C
|
| 28 |
+
ATOM 27 HD21 LEU A 2 9.914 2.946 -3.326 1.00 0.00 H
|
| 29 |
+
ATOM 28 HD22 LEU A 2 11.352 2.453 -2.400 1.00 0.00 H
|
| 30 |
+
ATOM 29 HD23 LEU A 2 9.914 1.405 -2.436 1.00 0.00 H
|
| 31 |
+
ATOM 30 C LEU A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 32 |
+
ATOM 31 O LEU A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 33 |
+
ATOM 32 N THR A 3 9.517 5.386 0.000 1.00 0.00 N
|
| 34 |
+
ATOM 33 H THR A 3 10.103 4.564 0.000 1.00 0.00 H
|
| 35 |
+
ATOM 34 CA THR A 3 10.161 6.684 0.000 1.00 0.00 C
|
| 36 |
+
ATOM 35 HA THR A 3 9.863 7.239 -0.890 1.00 0.00 H
|
| 37 |
+
ATOM 36 CB THR A 3 9.768 7.492 1.232 1.00 0.00 C
|
| 38 |
+
ATOM 37 HB THR A 3 10.266 8.462 1.206 1.00 0.00 H
|
| 39 |
+
ATOM 38 CG2 THR A 3 8.257 7.698 1.244 1.00 0.00 C
|
| 40 |
+
ATOM 39 HG21 THR A 3 7.758 6.729 1.271 1.00 0.00 H
|
| 41 |
+
ATOM 40 HG22 THR A 3 7.975 8.276 2.125 1.00 0.00 H
|
| 42 |
+
ATOM 41 HG23 THR A 3 7.956 8.236 0.346 1.00 0.00 H
|
| 43 |
+
ATOM 42 OG1 THR A 3 10.163 6.786 2.411 1.00 0.00 O
|
| 44 |
+
ATOM 43 HG1 THR A 3 9.915 7.295 3.187 1.00 0.00 H
|
| 45 |
+
ATOM 44 C THR A 3 11.677 6.544 0.000 1.00 0.00 C
|
| 46 |
+
ATOM 45 O THR A 3 12.200 5.432 0.000 1.00 0.00 O
|
| 47 |
+
ATOM 46 N VAL A 4 12.382 7.677 0.000 1.00 0.00 N
|
| 48 |
+
ATOM 47 H VAL A 4 11.906 8.568 0.000 1.00 0.00 H
|
| 49 |
+
ATOM 48 CA VAL A 4 13.831 7.677 0.000 1.00 0.00 C
|
| 50 |
+
ATOM 49 HA VAL A 4 14.195 7.163 0.890 1.00 0.00 H
|
| 51 |
+
ATOM 50 CB VAL A 4 14.380 6.966 -1.232 1.00 0.00 C
|
| 52 |
+
ATOM 51 HB VAL A 4 14.032 5.933 -1.241 1.00 0.00 H
|
| 53 |
+
ATOM 52 CG1 VAL A 4 13.892 7.678 -2.490 1.00 0.00 C
|
| 54 |
+
ATOM 53 HG11 VAL A 4 14.241 8.710 -2.481 1.00 0.00 H
|
| 55 |
+
ATOM 54 HG12 VAL A 4 14.284 7.170 -3.371 1.00 0.00 H
|
| 56 |
+
ATOM 55 HG13 VAL A 4 12.803 7.662 -2.517 1.00 0.00 H
|
| 57 |
+
ATOM 56 CG2 VAL A 4 15.904 6.987 -1.195 1.00 0.00 C
|
| 58 |
+
ATOM 57 HG21 VAL A 4 16.253 6.479 -0.296 1.00 0.00 H
|
| 59 |
+
ATOM 58 HG22 VAL A 4 16.297 6.479 -2.075 1.00 0.00 H
|
| 60 |
+
ATOM 59 HG23 VAL A 4 16.253 8.020 -1.186 1.00 0.00 H
|
| 61 |
+
ATOM 60 C VAL A 4 14.379 9.097 0.000 1.00 0.00 C
|
| 62 |
+
ATOM 61 O VAL A 4 13.616 10.060 0.000 1.00 0.00 O
|
| 63 |
+
ATOM 62 OXT VAL A 4 15.666 9.049 0.062 1.00 0.00 O
|
| 64 |
+
TER 63 VAL A 4
|
| 65 |
+
END
|
4AA-large/test/ALVE-traj-state0.pdb
ADDED
|
@@ -0,0 +1,66 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH OPENMM 7.7, 2022-09-02
|
| 2 |
+
ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ALA A 1 2.636 1.444 -0.983 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.501 1.315 0.845 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
|
| 11 |
+
ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 12 |
+
ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 13 |
+
ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 14 |
+
ATOM 13 N LEU A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H LEU A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA LEU A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA LEU A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 CB LEU A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 19 |
+
ATOM 18 HB2 LEU A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 20 |
+
ATOM 19 HB3 LEU A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 21 |
+
ATOM 20 CG LEU A 2 9.713 3.149 -1.195 1.00 0.00 C
|
| 22 |
+
ATOM 21 HG LEU A 2 10.062 4.181 -1.186 1.00 0.00 H
|
| 23 |
+
ATOM 22 CD1 LEU A 2 10.201 2.437 0.063 1.00 0.00 C
|
| 24 |
+
ATOM 23 HD11 LEU A 2 9.853 1.404 0.055 1.00 0.00 H
|
| 25 |
+
ATOM 24 HD12 LEU A 2 11.291 2.452 0.090 1.00 0.00 H
|
| 26 |
+
ATOM 25 HD13 LEU A 2 9.809 2.945 0.944 1.00 0.00 H
|
| 27 |
+
ATOM 26 CD2 LEU A 2 10.262 2.438 -2.427 1.00 0.00 C
|
| 28 |
+
ATOM 27 HD21 LEU A 2 9.914 2.946 -3.326 1.00 0.00 H
|
| 29 |
+
ATOM 28 HD22 LEU A 2 11.352 2.453 -2.400 1.00 0.00 H
|
| 30 |
+
ATOM 29 HD23 LEU A 2 9.914 1.405 -2.436 1.00 0.00 H
|
| 31 |
+
ATOM 30 C LEU A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 32 |
+
ATOM 31 O LEU A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 33 |
+
ATOM 32 N VAL A 3 9.517 5.386 0.000 1.00 0.00 N
|
| 34 |
+
ATOM 33 H VAL A 3 10.103 4.564 0.000 1.00 0.00 H
|
| 35 |
+
ATOM 34 CA VAL A 3 10.161 6.684 0.000 1.00 0.00 C
|
| 36 |
+
ATOM 35 HA VAL A 3 9.863 7.239 -0.890 1.00 0.00 H
|
| 37 |
+
ATOM 36 CB VAL A 3 9.768 7.492 1.232 1.00 0.00 C
|
| 38 |
+
ATOM 37 HB VAL A 3 8.688 7.640 1.241 1.00 0.00 H
|
| 39 |
+
ATOM 38 CG1 VAL A 3 10.189 6.739 2.490 1.00 0.00 C
|
| 40 |
+
ATOM 39 HG11 VAL A 3 11.269 6.592 2.481 1.00 0.00 H
|
| 41 |
+
ATOM 40 HG12 VAL A 3 9.908 7.316 3.371 1.00 0.00 H
|
| 42 |
+
ATOM 41 HG13 VAL A 3 9.691 5.770 2.517 1.00 0.00 H
|
| 43 |
+
ATOM 42 CG2 VAL A 3 10.465 8.848 1.195 1.00 0.00 C
|
| 44 |
+
ATOM 43 HG21 VAL A 3 10.165 9.387 0.296 1.00 0.00 H
|
| 45 |
+
ATOM 44 HG22 VAL A 3 10.185 9.426 2.075 1.00 0.00 H
|
| 46 |
+
ATOM 45 HG23 VAL A 3 11.545 8.702 1.186 1.00 0.00 H
|
| 47 |
+
ATOM 46 C VAL A 3 11.677 6.544 0.000 1.00 0.00 C
|
| 48 |
+
ATOM 47 O VAL A 3 12.200 5.432 0.000 1.00 0.00 O
|
| 49 |
+
ATOM 48 N GLU A 4 12.382 7.677 0.000 1.00 0.00 N
|
| 50 |
+
ATOM 49 H GLU A 4 11.906 8.568 0.000 1.00 0.00 H
|
| 51 |
+
ATOM 50 CA GLU A 4 13.831 7.677 0.000 1.00 0.00 C
|
| 52 |
+
ATOM 51 HA GLU A 4 14.195 7.163 0.890 1.00 0.00 H
|
| 53 |
+
ATOM 52 CB GLU A 4 14.380 6.966 -1.232 1.00 0.00 C
|
| 54 |
+
ATOM 53 HB2 GLU A 4 14.032 5.933 -1.241 1.00 0.00 H
|
| 55 |
+
ATOM 54 HB3 GLU A 4 14.032 7.474 -2.131 1.00 0.00 H
|
| 56 |
+
ATOM 55 CG GLU A 4 15.889 6.987 -1.195 1.00 0.00 C
|
| 57 |
+
ATOM 56 HG2 GLU A 4 16.238 8.020 -1.186 1.00 0.00 H
|
| 58 |
+
ATOM 57 HG3 GLU A 4 16.238 6.479 -0.296 1.00 0.00 H
|
| 59 |
+
ATOM 58 CD GLU A 4 16.439 6.275 -2.429 1.00 0.00 C
|
| 60 |
+
ATOM 59 OE1 GLU A 4 16.646 6.977 -3.454 1.00 0.00 O
|
| 61 |
+
ATOM 60 OE2 GLU A 4 16.646 5.036 -2.334 1.00 0.00 O
|
| 62 |
+
ATOM 61 C GLU A 4 14.379 9.097 0.000 1.00 0.00 C
|
| 63 |
+
ATOM 62 O GLU A 4 13.616 10.060 0.000 1.00 0.00 O
|
| 64 |
+
ATOM 63 OXT GLU A 4 15.666 9.052 0.061 1.00 0.00 O
|
| 65 |
+
TER 64 GLU A 4
|
| 66 |
+
END
|
4AA-large/test/AMIG-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:be8bd1c47f7aefcbfc3731a87f258fbee4f063a0162fa6cd1dd52b99e8fba45f
|
| 3 |
+
size 941397322
|
4AA-large/test/AMIG-traj-state0.pdb
ADDED
|
@@ -0,0 +1,59 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH OPENMM 7.7, 2022-09-01
|
| 2 |
+
ATOM 1 N ALA A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ALA A 1 2.493 1.309 0.836 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.642 1.454 -0.988 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB1 ALA A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB2 ALA A 1 4.075 4.623 1.206 1.00 0.00 H
|
| 11 |
+
ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 12 |
+
ATOM 11 C ALA A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 13 |
+
ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 14 |
+
ATOM 13 N MET A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H MET A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA MET A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA MET A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 CB MET A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 19 |
+
ATOM 18 HB2 MET A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 20 |
+
ATOM 19 HB3 MET A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 21 |
+
ATOM 20 CG MET A 2 9.713 3.149 -1.195 1.00 0.00 C
|
| 22 |
+
ATOM 21 HG2 MET A 2 10.062 4.181 -1.186 1.00 0.00 H
|
| 23 |
+
ATOM 22 HG3 MET A 2 10.062 2.640 -0.296 1.00 0.00 H
|
| 24 |
+
ATOM 23 SD MET A 2 10.381 2.308 -2.652 1.00 0.00 S
|
| 25 |
+
ATOM 24 CE MET A 2 12.124 2.487 -2.341 1.00 0.00 C
|
| 26 |
+
ATOM 25 HE1 MET A 2 12.377 2.005 -1.397 1.00 0.00 H
|
| 27 |
+
ATOM 26 HE2 MET A 2 12.688 2.021 -3.149 1.00 0.00 H
|
| 28 |
+
ATOM 27 HE3 MET A 2 12.377 3.546 -2.287 1.00 0.00 H
|
| 29 |
+
ATOM 28 C MET A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 30 |
+
ATOM 29 O MET A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 31 |
+
ATOM 30 N ILE A 3 9.517 5.386 0.000 1.00 0.00 N
|
| 32 |
+
ATOM 31 H ILE A 3 10.103 4.564 0.000 1.00 0.00 H
|
| 33 |
+
ATOM 32 CA ILE A 3 10.161 6.684 0.000 1.00 0.00 C
|
| 34 |
+
ATOM 33 HA ILE A 3 9.863 7.239 -0.890 1.00 0.00 H
|
| 35 |
+
ATOM 34 CB ILE A 3 9.743 7.459 1.245 1.00 0.00 C
|
| 36 |
+
ATOM 35 HB ILE A 3 8.661 7.591 1.246 1.00 0.00 H
|
| 37 |
+
ATOM 36 CG2 ILE A 3 10.161 6.684 2.490 1.00 0.00 C
|
| 38 |
+
ATOM 37 HG21 ILE A 3 11.243 6.553 2.491 1.00 0.00 H
|
| 39 |
+
ATOM 38 HG22 ILE A 3 9.863 7.238 3.381 1.00 0.00 H
|
| 40 |
+
ATOM 39 HG23 ILE A 3 9.677 5.708 2.491 1.00 0.00 H
|
| 41 |
+
ATOM 40 CG1 ILE A 3 10.421 8.825 1.245 1.00 0.00 C
|
| 42 |
+
ATOM 41 HG12 ILE A 3 11.503 8.694 1.245 1.00 0.00 H
|
| 43 |
+
ATOM 42 HG13 ILE A 3 10.123 9.380 0.355 1.00 0.00 H
|
| 44 |
+
ATOM 43 CD1 ILE A 3 10.003 9.600 2.490 1.00 0.00 C
|
| 45 |
+
ATOM 44 HD11 ILE A 3 10.302 9.047 3.381 1.00 0.00 H
|
| 46 |
+
ATOM 45 HD12 ILE A 3 10.488 10.577 2.491 1.00 0.00 H
|
| 47 |
+
ATOM 46 HD13 ILE A 3 8.921 9.732 2.491 1.00 0.00 H
|
| 48 |
+
ATOM 47 C ILE A 3 11.677 6.544 0.000 1.00 0.00 C
|
| 49 |
+
ATOM 48 O ILE A 3 12.200 5.432 0.000 1.00 0.00 O
|
| 50 |
+
ATOM 49 N GLY A 4 12.382 7.677 0.000 1.00 0.00 N
|
| 51 |
+
ATOM 50 H GLY A 4 11.906 8.568 0.000 1.00 0.00 H
|
| 52 |
+
ATOM 51 CA GLY A 4 13.831 7.677 0.000 1.00 0.00 C
|
| 53 |
+
ATOM 52 HA2 GLY A 4 14.195 7.163 0.890 1.00 0.00 H
|
| 54 |
+
ATOM 53 HA3 GLY A 4 14.195 7.163 -0.890 1.00 0.00 H
|
| 55 |
+
ATOM 54 C GLY A 4 14.362 9.104 0.000 1.00 0.00 C
|
| 56 |
+
ATOM 55 O GLY A 4 13.586 10.057 0.000 1.00 0.00 O
|
| 57 |
+
ATOM 56 OXT GLY A 4 15.647 9.043 -0.010 1.00 0.00 O
|
| 58 |
+
TER 57 GLY A 4
|
| 59 |
+
END
|
4AA-large/test/ANFG-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
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|
|
|
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|
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|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:b19bee7f4aec766dfb9dfd5d2d37fa7a4540705db69fa68adcd065308b3e45be
|
| 3 |
+
size 907205456
|