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- 2AA-complete/README.md +52 -0
- 2AA-complete/test/AC-traj-arrays.npz +3 -0
- 2AA-complete/test/AC-traj-state0.pdb +28 -0
- 2AA-complete/test/AD-traj-arrays.npz +3 -0
- 2AA-complete/test/AD-traj-state0.pdb +29 -0
- 2AA-complete/test/AH-traj-arrays.npz +3 -0
- 2AA-complete/test/AH-traj-state0.pdb +34 -0
- 2AA-complete/test/AM-traj-arrays.npz +3 -0
- 2AA-complete/test/AM-traj-state0.pdb +34 -0
- 2AA-complete/test/AN-traj-arrays.npz +3 -0
- 2AA-complete/test/AN-traj-state0.pdb +31 -0
- 2AA-complete/test/AP-traj-arrays.npz +3 -0
- 2AA-complete/test/AP-traj-state0.pdb +31 -0
- 2AA-complete/test/AR-traj-arrays.npz +3 -0
- 2AA-complete/test/AR-traj-state0.pdb +41 -0
- 2AA-complete/test/AT-traj-arrays.npz +3 -0
- 2AA-complete/test/AT-traj-state0.pdb +31 -0
- 2AA-complete/test/CK-traj-arrays.npz +3 -0
- 2AA-complete/test/CK-traj-state0.pdb +40 -0
- 2AA-complete/test/CN-traj-arrays.npz +3 -0
- 2AA-complete/test/CN-traj-state0.pdb +32 -0
- 2AA-complete/test/CR-traj-arrays.npz +3 -0
- 2AA-complete/test/CR-traj-state0.pdb +42 -0
- 2AA-complete/test/CS-traj-arrays.npz +3 -0
- 2AA-complete/test/CS-traj-state0.pdb +29 -0
- 2AA-complete/test/CW-traj-arrays.npz +3 -0
- 2AA-complete/test/CW-traj-state0.pdb +42 -0
- 2AA-complete/test/DH-traj-arrays.npz +3 -0
- 2AA-complete/test/DH-traj-state0.pdb +36 -0
- 2AA-complete/test/DK-traj-arrays.npz +3 -0
- 2AA-complete/test/DK-traj-state0.pdb +41 -0
- 2AA-complete/test/DL-traj-arrays.npz +3 -0
- 2AA-complete/test/DL-traj-state0.pdb +38 -0
- 2AA-complete/test/DW-traj-arrays.npz +3 -0
- 2AA-complete/test/DW-traj-state0.pdb +43 -0
- 2AA-complete/test/EK-traj-arrays.npz +3 -0
- 2AA-complete/test/EK-traj-state0.pdb +44 -0
- 2AA-complete/test/EL-traj-arrays.npz +3 -0
- 2AA-complete/test/EL-traj-state0.pdb +41 -0
- 2AA-complete/test/ET-traj-arrays.npz +3 -0
- 2AA-complete/test/ET-traj-state0.pdb +36 -0
- 2AA-complete/test/EV-traj-arrays.npz +3 -0
- 2AA-complete/test/EV-traj-state0.pdb +38 -0
- 2AA-complete/test/EW-traj-arrays.npz +3 -0
- 2AA-complete/test/EW-traj-state0.pdb +46 -0
- 2AA-complete/test/EY-traj-arrays.npz +3 -0
- 2AA-complete/test/EY-traj-state0.pdb +43 -0
- 2AA-complete/test/FA-traj-arrays.npz +3 -0
- 2AA-complete/test/FA-traj-state0.pdb +37 -0
- 2AA-complete/test/FF-traj-arrays.npz +3 -0
2AA-complete/README.md
ADDED
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# 2AA-1-complete "Two Amino Acid" data set
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This folder contains a data set of all-atom molecular dynamics trajectories for all 400
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dipeptides, i.e. small proteins composed of two amino acids.
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This includes also the peptides missing in the other 2AA datasets.
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Each peptide is simulated using classical molecular dynamics and the
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water is simulated using an implicit water model.
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For each protein 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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The NPZ file contains detailed information for a subset of simulation steps.
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There are T such frames and the NPZ file contains the following arrays:
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* 'time': `(T,)` array, simulation time in picoseconds.
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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. Construct initial protein using AmberTools's `tleap` program.
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2. Process each PDB file using [pdbfixer](https://github.com/openmm/pdbfixer),
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adding all missing hydrogen atoms. This is the `state0.pdb` file.
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3. For each all-atom PDB file, perform a molecular dynamics simulation:
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a.) Use OpenMM with the AMBER99 force field and implicit water model.
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b.) Perform an energy minimization (relaxation) from the initial extended
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configuration.
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c.) Use a second-order Langevin integrator at temperature to T=310K,
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friction=0.3/ps, timestep=1.0fs for 50,000 steps to equilibriate
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("burn-in phase").
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d.) Use a second-order Langevin integrator at temperature to T=310K,
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friction=0.3/ps, timestep=1.0fs for 5e6 steps to sample a trajectory
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("sample phase").
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4. Save trajectory information to an `arrays.npz` file.
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5. Shuffle and partition the trajectories into a `train` set
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(200 trajectories), `val` (80 trajectories), and `test` (100 trajectories).
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## Credit and Authors
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This dataset was created in October 2022 as part of Timewarp.
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2AA-complete/test/AC-traj-arrays.npz
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version https://git-lfs.github.com/spec/v1
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oid sha256:22d0f24709d3ec655dfdd71aa7af9fa0edd3bf48e647c06c7da7bd4dc89b037f
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size 8782296
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2AA-complete/test/AC-traj-state0.pdb
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MODEL 0
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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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ATOM 2 H2 ALA A 1 2.646 1.449 -0.990 1.00 0.00 H
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| 4 |
+
ATOM 3 H3 ALA A 1 2.495 1.312 0.839 1.00 0.00 H
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| 5 |
+
ATOM 4 H ALA A 1 3.909 0.724 0.000 1.00 0.00 H
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| 6 |
+
ATOM 5 CA ALA A 1 3.970 2.846 0.000 1.00 0.00 C
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| 7 |
+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
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| 8 |
+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
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| 9 |
+
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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| 11 |
+
ATOM 10 HB3 ALA A 1 2.497 3.801 1.241 1.00 0.00 H
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| 12 |
+
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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| 14 |
+
ATOM 13 N CYS A 2 6.191 3.839 0.000 1.00 0.00 N
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| 15 |
+
ATOM 14 H CYS A 2 5.715 4.730 0.000 1.00 0.00 H
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| 16 |
+
ATOM 15 CA CYS A 2 7.640 3.839 0.000 1.00 0.00 C
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| 17 |
+
ATOM 16 HA CYS A 2 8.004 3.325 0.890 1.00 0.00 H
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| 18 |
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ATOM 17 CB CYS A 2 8.189 3.127 -1.232 1.00 0.00 C
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| 19 |
+
ATOM 18 HB2 CYS A 2 7.841 2.094 -1.241 1.00 0.00 H
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| 20 |
+
ATOM 19 HB3 CYS A 2 7.841 3.636 -2.131 1.00 0.00 H
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ATOM 20 SG CYS A 2 9.992 3.050 -1.366 1.00 0.00 S
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ATOM 21 HG CYS A 2 10.018 2.385 -2.518 1.00 0.00 H
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| 23 |
+
ATOM 22 C CYS A 2 8.188 5.259 0.000 1.00 0.00 C
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| 24 |
+
ATOM 23 O CYS A 2 7.425 6.222 0.000 1.00 0.00 O
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+
ATOM 24 OXT CYS A 2 9.441 5.317 0.056 1.00 0.00 O
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+
TER 25 CYS A 2
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ENDMDL
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END
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2AA-complete/test/AD-traj-arrays.npz
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version https://git-lfs.github.com/spec/v1
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oid sha256:9b2aefbb048baacc5253a93662add8e77ef9563e7ab7275701988b83e5b0a105
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+
size 9135096
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2AA-complete/test/AD-traj-state0.pdb
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MODEL 0
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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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ATOM 2 H2 ALA A 1 2.494 1.313 0.838 1.00 0.00 H
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| 4 |
+
ATOM 3 H3 ALA A 1 2.644 1.442 -0.988 1.00 0.00 H
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| 5 |
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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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| 6 |
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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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| 7 |
+
ATOM 6 HA ALA A 1 3.672 3.400 -0.890 1.00 0.00 H
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| 8 |
+
ATOM 7 CB ALA A 1 3.577 3.654 1.232 1.00 0.00 C
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| 9 |
+
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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| 11 |
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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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+
ATOM 12 O ALA A 1 6.009 1.593 0.000 1.00 0.00 O
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ATOM 13 N ASP A 2 6.191 3.839 0.000 1.00 0.00 N
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| 15 |
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ATOM 14 H ASP A 2 5.715 4.730 0.000 1.00 0.00 H
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| 16 |
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ATOM 15 CA ASP A 2 7.640 3.839 0.000 1.00 0.00 C
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| 17 |
+
ATOM 16 HA ASP A 2 8.004 3.325 0.890 1.00 0.00 H
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| 18 |
+
ATOM 17 CB ASP A 2 8.189 3.127 -1.232 1.00 0.00 C
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| 19 |
+
ATOM 18 HB2 ASP A 2 7.841 2.094 -1.241 1.00 0.00 H
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| 20 |
+
ATOM 19 HB3 ASP A 2 7.841 3.636 -2.131 1.00 0.00 H
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| 21 |
+
ATOM 20 CG ASP A 2 9.715 3.149 -1.195 1.00 0.00 C
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| 22 |
+
ATOM 21 OD1 ASP A 2 10.291 2.187 -0.620 1.00 0.00 O
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| 23 |
+
ATOM 22 OD2 ASP A 2 10.291 4.128 -1.741 1.00 0.00 O
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| 24 |
+
ATOM 23 C ASP A 2 8.188 5.259 0.000 1.00 0.00 C
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| 25 |
+
ATOM 24 O ASP A 2 7.425 6.222 0.000 1.00 0.00 O
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ATOM 25 OXT ASP A 2 9.435 5.329 0.115 1.00 0.00 O
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TER 26 ASP A 2
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ENDMDL
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END
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2AA-complete/test/AH-traj-arrays.npz
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version https://git-lfs.github.com/spec/v1
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oid sha256:74d2e4329bfb5eff67b65231fea7f7f4054f975be2bc6fbaca84cde40654e672
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| 3 |
+
size 10899096
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2AA-complete/test/AH-traj-state0.pdb
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MODEL 0
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| 2 |
+
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 2.640 1.450 -0.987 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.493 1.313 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 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
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| 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
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| 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 OXT HIS A 2 9.436 5.326 0.097 1.00 0.00 O
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| 32 |
+
TER 31 HIS A 2
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| 33 |
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ENDMDL
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| 34 |
+
END
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2AA-complete/test/AM-traj-arrays.npz
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version https://git-lfs.github.com/spec/v1
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oid sha256:e603a699efbb5a2025e460c5b748a189edbb58a27b058b53dccc60f89aabf8f7
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| 3 |
+
size 10899096
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2AA-complete/test/AM-traj-state0.pdb
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MODEL 0
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| 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 1.451 -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 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 OXT MET A 2 9.440 5.322 0.069 1.00 0.00 O
|
| 32 |
+
TER 31 MET A 2
|
| 33 |
+
ENDMDL
|
| 34 |
+
END
|
2AA-complete/test/AN-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:8ec51b0984e560c4465a8c4a1f170fba69566b02d8aa9585755282c05133a342
|
| 3 |
+
size 9840696
|
2AA-complete/test/AN-traj-state0.pdb
ADDED
|
@@ -0,0 +1,31 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
MODEL 0
|
| 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 2.496 1.311 0.838 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 ASN A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H ASN A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA ASN A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA ASN A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 CB ASN A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 19 |
+
ATOM 18 HB2 ASN A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 20 |
+
ATOM 19 HB3 ASN A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 21 |
+
ATOM 20 CG ASN A 2 9.711 3.127 -1.232 1.00 0.00 C
|
| 22 |
+
ATOM 21 OD1 ASN A 2 10.335 3.657 -0.315 1.00 0.00 O
|
| 23 |
+
ATOM 22 ND2 ASN A 2 10.309 2.530 -2.266 1.00 0.00 N
|
| 24 |
+
ATOM 23 HD21 ASN A 2 11.317 2.502 -2.315 1.00 0.00 H
|
| 25 |
+
ATOM 24 HD22 ASN A 2 9.750 2.110 -2.994 1.00 0.00 H
|
| 26 |
+
ATOM 25 C ASN A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 27 |
+
ATOM 26 O ASN A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 28 |
+
ATOM 27 OXT ASN A 2 9.437 5.332 0.081 1.00 0.00 O
|
| 29 |
+
TER 28 ASN A 2
|
| 30 |
+
ENDMDL
|
| 31 |
+
END
|
2AA-complete/test/AP-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:819c0a0238174e2d3dce589dddcd8e68a3470e00e312eb103a5a9f9f079144fd
|
| 3 |
+
size 9840696
|
2AA-complete/test/AP-traj-state0.pdb
ADDED
|
@@ -0,0 +1,31 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
MODEL 0
|
| 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 1.304 0.834 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.645 1.443 -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 PRO A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 CD PRO A 2 5.547 5.147 0.000 1.00 0.00 C
|
| 16 |
+
ATOM 15 HD2 PRO A 2 5.240 5.401 1.014 1.00 0.00 H
|
| 17 |
+
ATOM 16 HD3 PRO A 2 4.672 5.121 -0.649 1.00 0.00 H
|
| 18 |
+
ATOM 17 CG PRO A 2 6.620 6.056 -0.522 1.00 0.00 C
|
| 19 |
+
ATOM 18 HG2 PRO A 2 6.576 7.003 0.016 1.00 0.00 H
|
| 20 |
+
ATOM 19 HG3 PRO A 2 6.470 6.237 -1.586 1.00 0.00 H
|
| 21 |
+
ATOM 20 CB PRO A 2 7.927 5.342 -0.276 1.00 0.00 C
|
| 22 |
+
ATOM 21 HB2 PRO A 2 8.424 5.789 0.586 1.00 0.00 H
|
| 23 |
+
ATOM 22 HB3 PRO A 2 8.564 5.445 -1.155 1.00 0.00 H
|
| 24 |
+
ATOM 23 CA PRO A 2 7.642 3.839 0.000 1.00 0.00 C
|
| 25 |
+
ATOM 24 HA PRO A 2 8.040 3.343 -0.886 1.00 0.00 H
|
| 26 |
+
ATOM 25 C PRO A 2 8.189 3.161 1.248 1.00 0.00 C
|
| 27 |
+
ATOM 26 O PRO A 2 7.426 2.647 2.064 1.00 0.00 O
|
| 28 |
+
ATOM 27 OXT PRO A 2 9.443 3.188 1.323 1.00 0.00 O
|
| 29 |
+
TER 28 PRO A 2
|
| 30 |
+
ENDMDL
|
| 31 |
+
END
|
2AA-complete/test/AR-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:92086fd5ba1d41d1b8fa73722ccbe9588a3c64d533964c747adf1b3a9f0b6276
|
| 3 |
+
size 13368696
|
2AA-complete/test/AR-traj-state0.pdb
ADDED
|
@@ -0,0 +1,41 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
MODEL 0
|
| 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 2.641 1.443 -0.986 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ALA A 1 2.496 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 ARG A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H ARG A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA ARG A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA ARG A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 CB ARG A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 19 |
+
ATOM 18 HB2 ARG A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 20 |
+
ATOM 19 HB3 ARG A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 21 |
+
ATOM 20 CG ARG A 2 9.713 3.149 -1.195 1.00 0.00 C
|
| 22 |
+
ATOM 21 HG2 ARG A 2 10.062 4.181 -1.186 1.00 0.00 H
|
| 23 |
+
ATOM 22 HG3 ARG A 2 10.062 2.640 -0.296 1.00 0.00 H
|
| 24 |
+
ATOM 23 CD ARG A 2 10.262 2.438 -2.427 1.00 0.00 C
|
| 25 |
+
ATOM 24 HD2 ARG A 2 9.914 1.405 -2.436 1.00 0.00 H
|
| 26 |
+
ATOM 25 HD3 ARG A 2 9.914 2.946 -3.326 1.00 0.00 H
|
| 27 |
+
ATOM 26 NE ARG A 2 11.742 2.439 -2.424 1.00 0.00 N
|
| 28 |
+
ATOM 27 HE ARG A 2 12.223 2.883 -1.655 1.00 0.00 H
|
| 29 |
+
ATOM 28 CZ ARG A 2 12.469 1.882 -3.389 1.00 0.00 C
|
| 30 |
+
ATOM 29 NH1 ARG A 2 11.909 1.279 -4.434 1.00 0.00 N
|
| 31 |
+
ATOM 30 HH11 ARG A 2 10.902 1.235 -4.509 1.00 0.00 H
|
| 32 |
+
ATOM 31 HH12 ARG A 2 12.492 0.866 -5.148 1.00 0.00 H
|
| 33 |
+
ATOM 32 NH2 ARG A 2 13.793 1.941 -3.287 1.00 0.00 N
|
| 34 |
+
ATOM 33 HH21 ARG A 2 14.215 2.400 -2.492 1.00 0.00 H
|
| 35 |
+
ATOM 34 HH22 ARG A 2 14.371 1.527 -4.004 1.00 0.00 H
|
| 36 |
+
ATOM 35 C ARG A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 37 |
+
ATOM 36 O ARG A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 38 |
+
ATOM 37 OXT ARG A 2 9.439 5.324 0.075 1.00 0.00 O
|
| 39 |
+
TER 38 ARG A 2
|
| 40 |
+
ENDMDL
|
| 41 |
+
END
|
2AA-complete/test/AT-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:8ed5e7f77538b9db65d824cd3b92f74f1ae6618eda9f0adc5c80f1c9f32fa587
|
| 3 |
+
size 9840696
|
2AA-complete/test/AT-traj-state0.pdb
ADDED
|
@@ -0,0 +1,31 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
MODEL 0
|
| 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 2.629 1.451 -0.978 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 THR A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 15 |
+
ATOM 14 H THR A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 16 |
+
ATOM 15 CA THR A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 17 |
+
ATOM 16 HA THR A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 18 |
+
ATOM 17 CB THR A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 19 |
+
ATOM 18 HB THR A 2 9.279 3.142 -1.206 1.00 0.00 H
|
| 20 |
+
ATOM 19 CG2 THR A 2 7.701 1.682 -1.244 1.00 0.00 C
|
| 21 |
+
ATOM 20 HG21 THR A 2 6.612 1.666 -1.271 1.00 0.00 H
|
| 22 |
+
ATOM 21 HG22 THR A 2 8.093 1.173 -2.125 1.00 0.00 H
|
| 23 |
+
ATOM 22 HG23 THR A 2 8.050 1.173 -0.346 1.00 0.00 H
|
| 24 |
+
ATOM 23 OG1 THR A 2 7.732 3.795 -2.411 1.00 0.00 O
|
| 25 |
+
ATOM 24 HG1 THR A 2 8.077 3.347 -3.187 1.00 0.00 H
|
| 26 |
+
ATOM 25 C THR A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 27 |
+
ATOM 26 O THR A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 28 |
+
ATOM 27 OXT THR A 2 9.443 5.318 0.044 1.00 0.00 O
|
| 29 |
+
TER 28 THR A 2
|
| 30 |
+
ENDMDL
|
| 31 |
+
END
|
2AA-complete/test/CK-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:66a89dd6d1fee8307acdf5a5096dcdb89ef65d9351c9eb952a9a1ff8076652dc
|
| 3 |
+
size 13015896
|
2AA-complete/test/CK-traj-state0.pdb
ADDED
|
@@ -0,0 +1,40 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
MODEL 0
|
| 2 |
+
ATOM 1 N CYS A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 CYS A 1 2.509 1.310 0.852 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 CYS A 1 2.632 1.453 -0.981 1.00 0.00 H
|
| 5 |
+
ATOM 4 H CYS A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA CYS A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA CYS A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB CYS A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB2 CYS A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB3 CYS A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 11 |
+
ATOM 10 SG CYS A 1 4.310 5.304 1.366 1.00 0.00 S
|
| 12 |
+
ATOM 11 HG CYS A 1 3.725 5.622 2.518 1.00 0.00 H
|
| 13 |
+
ATOM 12 C CYS A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 14 |
+
ATOM 13 O CYS A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 15 |
+
ATOM 14 N LYS A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 16 |
+
ATOM 15 H LYS A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 17 |
+
ATOM 16 CA LYS A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 18 |
+
ATOM 17 HA LYS A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 19 |
+
ATOM 18 CB LYS A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 20 |
+
ATOM 19 HB2 LYS A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 21 |
+
ATOM 20 HB3 LYS A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 22 |
+
ATOM 21 CG LYS A 2 9.713 3.149 -1.195 1.00 0.00 C
|
| 23 |
+
ATOM 22 HG2 LYS A 2 10.062 4.181 -1.186 1.00 0.00 H
|
| 24 |
+
ATOM 23 HG3 LYS A 2 10.062 2.640 -0.296 1.00 0.00 H
|
| 25 |
+
ATOM 24 CD LYS A 2 10.262 2.438 -2.427 1.00 0.00 C
|
| 26 |
+
ATOM 25 HD2 LYS A 2 9.914 1.405 -2.436 1.00 0.00 H
|
| 27 |
+
ATOM 26 HD3 LYS A 2 9.914 2.946 -3.326 1.00 0.00 H
|
| 28 |
+
ATOM 27 CE LYS A 2 11.787 2.459 -2.389 1.00 0.00 C
|
| 29 |
+
ATOM 28 HE2 LYS A 2 12.136 3.492 -2.380 1.00 0.00 H
|
| 30 |
+
ATOM 29 HE3 LYS A 2 12.136 1.951 -1.491 1.00 0.00 H
|
| 31 |
+
ATOM 30 NZ LYS A 2 12.316 1.773 -3.577 1.00 0.00 N
|
| 32 |
+
ATOM 31 HZ1 LYS A 2 11.993 2.245 -4.410 1.00 0.00 H
|
| 33 |
+
ATOM 32 HZ2 LYS A 2 13.326 1.788 -3.552 1.00 0.00 H
|
| 34 |
+
ATOM 33 HZ3 LYS A 2 11.993 0.817 -3.585 1.00 0.00 H
|
| 35 |
+
ATOM 34 C LYS A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 36 |
+
ATOM 35 O LYS A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 37 |
+
ATOM 36 OXT LYS A 2 9.440 5.325 0.067 1.00 0.00 O
|
| 38 |
+
TER 37 LYS A 2
|
| 39 |
+
ENDMDL
|
| 40 |
+
END
|
2AA-complete/test/CN-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:db89cb08471b0f251d4028e78a89bacd6a52034ea10ff4801e65bf43bdd96a78
|
| 3 |
+
size 10193496
|
2AA-complete/test/CN-traj-state0.pdb
ADDED
|
@@ -0,0 +1,32 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
MODEL 0
|
| 2 |
+
ATOM 1 N CYS A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 CYS A 1 2.640 1.453 -0.986 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 CYS A 1 2.497 1.309 0.840 1.00 0.00 H
|
| 5 |
+
ATOM 4 H CYS A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA CYS A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA CYS A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB CYS A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB2 CYS A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB3 CYS A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 11 |
+
ATOM 10 SG CYS A 1 4.310 5.304 1.366 1.00 0.00 S
|
| 12 |
+
ATOM 11 HG CYS A 1 3.725 5.622 2.518 1.00 0.00 H
|
| 13 |
+
ATOM 12 C CYS A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 14 |
+
ATOM 13 O CYS A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 15 |
+
ATOM 14 N ASN A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 16 |
+
ATOM 15 H ASN A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 17 |
+
ATOM 16 CA ASN A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 18 |
+
ATOM 17 HA ASN A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 19 |
+
ATOM 18 CB ASN A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 20 |
+
ATOM 19 HB2 ASN A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 21 |
+
ATOM 20 HB3 ASN A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 22 |
+
ATOM 21 CG ASN A 2 9.711 3.127 -1.232 1.00 0.00 C
|
| 23 |
+
ATOM 22 OD1 ASN A 2 10.335 3.657 -0.315 1.00 0.00 O
|
| 24 |
+
ATOM 23 ND2 ASN A 2 10.309 2.530 -2.266 1.00 0.00 N
|
| 25 |
+
ATOM 24 HD21 ASN A 2 11.317 2.502 -2.315 1.00 0.00 H
|
| 26 |
+
ATOM 25 HD22 ASN A 2 9.750 2.110 -2.994 1.00 0.00 H
|
| 27 |
+
ATOM 26 C ASN A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 28 |
+
ATOM 27 O ASN A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 29 |
+
ATOM 28 OXT ASN A 2 9.438 5.333 0.074 1.00 0.00 O
|
| 30 |
+
TER 29 ASN A 2
|
| 31 |
+
ENDMDL
|
| 32 |
+
END
|
2AA-complete/test/CR-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:2dcbb5f6ef5d2192fad71856e8879f3c73e2f73db30ee802a27b3cde07b0e794
|
| 3 |
+
size 13721496
|
2AA-complete/test/CR-traj-state0.pdb
ADDED
|
@@ -0,0 +1,42 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
MODEL 0
|
| 2 |
+
ATOM 1 N CYS A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 CYS A 1 2.640 1.445 -0.985 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 CYS A 1 2.498 1.309 0.841 1.00 0.00 H
|
| 5 |
+
ATOM 4 H CYS A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA CYS A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA CYS A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB CYS A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB2 CYS A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB3 CYS A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 11 |
+
ATOM 10 SG CYS A 1 4.310 5.304 1.366 1.00 0.00 S
|
| 12 |
+
ATOM 11 HG CYS A 1 3.725 5.622 2.518 1.00 0.00 H
|
| 13 |
+
ATOM 12 C CYS A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 14 |
+
ATOM 13 O CYS A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 15 |
+
ATOM 14 N ARG A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 16 |
+
ATOM 15 H ARG A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 17 |
+
ATOM 16 CA ARG A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 18 |
+
ATOM 17 HA ARG A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 19 |
+
ATOM 18 CB ARG A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 20 |
+
ATOM 19 HB2 ARG A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 21 |
+
ATOM 20 HB3 ARG A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 22 |
+
ATOM 21 CG ARG A 2 9.713 3.149 -1.195 1.00 0.00 C
|
| 23 |
+
ATOM 22 HG2 ARG A 2 10.062 4.181 -1.186 1.00 0.00 H
|
| 24 |
+
ATOM 23 HG3 ARG A 2 10.062 2.640 -0.296 1.00 0.00 H
|
| 25 |
+
ATOM 24 CD ARG A 2 10.262 2.438 -2.427 1.00 0.00 C
|
| 26 |
+
ATOM 25 HD2 ARG A 2 9.914 1.405 -2.436 1.00 0.00 H
|
| 27 |
+
ATOM 26 HD3 ARG A 2 9.914 2.946 -3.326 1.00 0.00 H
|
| 28 |
+
ATOM 27 NE ARG A 2 11.742 2.439 -2.424 1.00 0.00 N
|
| 29 |
+
ATOM 28 HE ARG A 2 12.223 2.883 -1.655 1.00 0.00 H
|
| 30 |
+
ATOM 29 CZ ARG A 2 12.469 1.882 -3.389 1.00 0.00 C
|
| 31 |
+
ATOM 30 NH1 ARG A 2 11.909 1.279 -4.434 1.00 0.00 N
|
| 32 |
+
ATOM 31 HH11 ARG A 2 10.902 1.235 -4.509 1.00 0.00 H
|
| 33 |
+
ATOM 32 HH12 ARG A 2 12.492 0.866 -5.148 1.00 0.00 H
|
| 34 |
+
ATOM 33 NH2 ARG A 2 13.793 1.941 -3.287 1.00 0.00 N
|
| 35 |
+
ATOM 34 HH21 ARG A 2 14.215 2.400 -2.492 1.00 0.00 H
|
| 36 |
+
ATOM 35 HH22 ARG A 2 14.371 1.527 -4.004 1.00 0.00 H
|
| 37 |
+
ATOM 36 C ARG A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 38 |
+
ATOM 37 O ARG A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 39 |
+
ATOM 38 OXT ARG A 2 9.440 5.325 0.068 1.00 0.00 O
|
| 40 |
+
TER 39 ARG A 2
|
| 41 |
+
ENDMDL
|
| 42 |
+
END
|
2AA-complete/test/CS-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:81bc4bf0c9197713f31c5d70781e47a885349d349138e44e245975b6687afca9
|
| 3 |
+
size 9135096
|
2AA-complete/test/CS-traj-state0.pdb
ADDED
|
@@ -0,0 +1,29 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
MODEL 0
|
| 2 |
+
ATOM 1 N CYS A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 CYS A 1 2.495 1.315 0.840 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 CYS A 1 2.642 1.445 -0.987 1.00 0.00 H
|
| 5 |
+
ATOM 4 H CYS A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA CYS A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA CYS A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB CYS A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB2 CYS A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB3 CYS A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 11 |
+
ATOM 10 SG CYS A 1 4.310 5.304 1.366 1.00 0.00 S
|
| 12 |
+
ATOM 11 HG CYS A 1 3.725 5.622 2.518 1.00 0.00 H
|
| 13 |
+
ATOM 12 C CYS A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 14 |
+
ATOM 13 O CYS A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 15 |
+
ATOM 14 N SER A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 16 |
+
ATOM 15 H SER A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 17 |
+
ATOM 16 CA SER A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 18 |
+
ATOM 17 HA SER A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 19 |
+
ATOM 18 CB SER A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 20 |
+
ATOM 19 HB2 SER A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 21 |
+
ATOM 20 HB3 SER A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 22 |
+
ATOM 21 OG SER A 2 9.618 3.148 -1.197 1.00 0.00 O
|
| 23 |
+
ATOM 22 HG SER A 2 9.964 2.700 -1.973 1.00 0.00 H
|
| 24 |
+
ATOM 23 C SER A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 25 |
+
ATOM 24 O SER A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 26 |
+
ATOM 25 OXT SER A 2 9.441 5.322 0.052 1.00 0.00 O
|
| 27 |
+
TER 26 SER A 2
|
| 28 |
+
ENDMDL
|
| 29 |
+
END
|
2AA-complete/test/CW-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:b7ad25abc429cf8acfe671313253ff0edae1a926d9058729fe3b963ef3be2ab6
|
| 3 |
+
size 13721496
|
2AA-complete/test/CW-traj-state0.pdb
ADDED
|
@@ -0,0 +1,42 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
MODEL 0
|
| 2 |
+
ATOM 1 N CYS A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 CYS A 1 2.495 1.314 0.839 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 CYS A 1 2.644 1.444 -0.989 1.00 0.00 H
|
| 5 |
+
ATOM 4 H CYS A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA CYS A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA CYS A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB CYS A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB2 CYS A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB3 CYS A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 11 |
+
ATOM 10 SG CYS A 1 4.310 5.304 1.366 1.00 0.00 S
|
| 12 |
+
ATOM 11 HG CYS A 1 3.725 5.622 2.518 1.00 0.00 H
|
| 13 |
+
ATOM 12 C CYS A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 14 |
+
ATOM 13 O CYS A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 15 |
+
ATOM 14 N TRP A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 16 |
+
ATOM 15 H TRP A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 17 |
+
ATOM 16 CA TRP A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 18 |
+
ATOM 17 HA TRP A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 19 |
+
ATOM 18 CB TRP A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 20 |
+
ATOM 19 HB2 TRP A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 21 |
+
ATOM 20 HB3 TRP A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 22 |
+
ATOM 21 CG TRP A 2 9.696 3.076 -1.321 1.00 0.00 C
|
| 23 |
+
ATOM 22 CD1 TRP A 2 10.427 2.515 -2.293 1.00 0.00 C
|
| 24 |
+
ATOM 23 HD1 TRP A 2 9.934 2.029 -3.135 1.00 0.00 H
|
| 25 |
+
ATOM 24 NE1 TRP A 2 11.801 2.713 -1.950 1.00 0.00 N
|
| 26 |
+
ATOM 25 HE1 TRP A 2 12.593 2.399 -2.493 1.00 0.00 H
|
| 27 |
+
ATOM 26 CE2 TRP A 2 11.867 3.367 -0.817 1.00 0.00 C
|
| 28 |
+
ATOM 27 CZ2 TRP A 2 13.013 3.770 -0.120 1.00 0.00 C
|
| 29 |
+
ATOM 28 HZ2 TRP A 2 14.002 3.540 -0.517 1.00 0.00 H
|
| 30 |
+
ATOM 29 CH2 TRP A 2 12.793 4.456 1.069 1.00 0.00 C
|
| 31 |
+
ATOM 30 HH2 TRP A 2 13.639 4.799 1.664 1.00 0.00 H
|
| 32 |
+
ATOM 31 CZ3 TRP A 2 11.540 4.708 1.505 1.00 0.00 C
|
| 33 |
+
ATOM 32 HZ3 TRP A 2 11.387 5.247 2.440 1.00 0.00 H
|
| 34 |
+
ATOM 33 CE3 TRP A 2 10.401 4.292 0.786 1.00 0.00 C
|
| 35 |
+
ATOM 34 HE3 TRP A 2 9.405 4.513 1.168 1.00 0.00 H
|
| 36 |
+
ATOM 35 CD2 TRP A 2 10.623 3.601 -0.412 1.00 0.00 C
|
| 37 |
+
ATOM 36 C TRP A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 38 |
+
ATOM 37 O TRP A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 39 |
+
ATOM 38 OXT TRP A 2 9.436 5.329 0.036 1.00 0.00 O
|
| 40 |
+
TER 39 TRP A 2
|
| 41 |
+
ENDMDL
|
| 42 |
+
END
|
2AA-complete/test/DH-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:56242149f34edd1001e36821598beaf9c345e660a72abde04caa1a6b58f0675c
|
| 3 |
+
size 11604696
|
2AA-complete/test/DH-traj-state0.pdb
ADDED
|
@@ -0,0 +1,36 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
MODEL 0
|
| 2 |
+
ATOM 1 N ASP A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ASP A 1 2.644 1.448 -0.988 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ASP A 1 2.494 1.309 0.837 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ASP A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ASP A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ASP A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ASP A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB2 ASP A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB3 ASP A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 11 |
+
ATOM 10 CG ASP A 1 4.275 5.011 1.195 1.00 0.00 C
|
| 12 |
+
ATOM 11 OD1 ASP A 1 3.669 5.955 0.620 1.00 0.00 O
|
| 13 |
+
ATOM 12 OD2 ASP A 1 5.408 5.092 1.741 1.00 0.00 O
|
| 14 |
+
ATOM 13 C ASP A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 15 |
+
ATOM 14 O ASP A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 16 |
+
ATOM 15 N HIS A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 17 |
+
ATOM 16 H HIS A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 18 |
+
ATOM 17 CA HIS A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 19 |
+
ATOM 18 HA HIS A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 20 |
+
ATOM 19 CB HIS A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 21 |
+
ATOM 20 HB2 HIS A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 22 |
+
ATOM 21 HB3 HIS A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 23 |
+
ATOM 22 CG HIS A 2 9.696 3.076 -1.321 1.00 0.00 C
|
| 24 |
+
ATOM 23 ND1 HIS A 2 10.350 2.463 -2.383 1.00 0.00 N
|
| 25 |
+
ATOM 24 CE1 HIS A 2 11.650 2.579 -2.183 1.00 0.00 C
|
| 26 |
+
ATOM 25 HE1 HIS A 2 12.352 2.162 -2.905 1.00 0.00 H
|
| 27 |
+
ATOM 26 NE2 HIS A 2 11.852 3.226 -1.062 1.00 0.00 N
|
| 28 |
+
ATOM 27 HE2 HIS A 2 12.759 3.448 -0.677 1.00 0.00 H
|
| 29 |
+
ATOM 28 CD2 HIS A 2 10.662 3.554 -0.492 1.00 0.00 C
|
| 30 |
+
ATOM 29 HD2 HIS A 2 10.641 4.099 0.451 1.00 0.00 H
|
| 31 |
+
ATOM 30 C HIS A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 32 |
+
ATOM 31 O HIS A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 33 |
+
ATOM 32 OXT HIS A 2 9.437 5.331 0.078 1.00 0.00 O
|
| 34 |
+
TER 33 HIS A 2
|
| 35 |
+
ENDMDL
|
| 36 |
+
END
|
2AA-complete/test/DK-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:4b2d1ab74c6d548cb2bef5f8e15a63589b614e3d70911eeb7f103df5a17cc159
|
| 3 |
+
size 13368696
|
2AA-complete/test/DK-traj-state0.pdb
ADDED
|
@@ -0,0 +1,41 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
MODEL 0
|
| 2 |
+
ATOM 1 N ASP A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ASP A 1 2.633 1.451 -0.981 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ASP A 1 2.507 1.317 0.852 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ASP A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ASP A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ASP A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ASP A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB2 ASP A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB3 ASP A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 11 |
+
ATOM 10 CG ASP A 1 4.275 5.011 1.195 1.00 0.00 C
|
| 12 |
+
ATOM 11 OD1 ASP A 1 3.669 5.955 0.620 1.00 0.00 O
|
| 13 |
+
ATOM 12 OD2 ASP A 1 5.408 5.092 1.741 1.00 0.00 O
|
| 14 |
+
ATOM 13 C ASP A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 15 |
+
ATOM 14 O ASP A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 16 |
+
ATOM 15 N LYS A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 17 |
+
ATOM 16 H LYS A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 18 |
+
ATOM 17 CA LYS A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 19 |
+
ATOM 18 HA LYS A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 20 |
+
ATOM 19 CB LYS A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 21 |
+
ATOM 20 HB2 LYS A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 22 |
+
ATOM 21 HB3 LYS A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 23 |
+
ATOM 22 CG LYS A 2 9.713 3.149 -1.195 1.00 0.00 C
|
| 24 |
+
ATOM 23 HG2 LYS A 2 10.062 4.181 -1.186 1.00 0.00 H
|
| 25 |
+
ATOM 24 HG3 LYS A 2 10.062 2.640 -0.296 1.00 0.00 H
|
| 26 |
+
ATOM 25 CD LYS A 2 10.262 2.438 -2.427 1.00 0.00 C
|
| 27 |
+
ATOM 26 HD2 LYS A 2 9.914 1.405 -2.436 1.00 0.00 H
|
| 28 |
+
ATOM 27 HD3 LYS A 2 9.914 2.946 -3.326 1.00 0.00 H
|
| 29 |
+
ATOM 28 CE LYS A 2 11.787 2.459 -2.389 1.00 0.00 C
|
| 30 |
+
ATOM 29 HE2 LYS A 2 12.136 3.492 -2.380 1.00 0.00 H
|
| 31 |
+
ATOM 30 HE3 LYS A 2 12.136 1.951 -1.491 1.00 0.00 H
|
| 32 |
+
ATOM 31 NZ LYS A 2 12.316 1.773 -3.577 1.00 0.00 N
|
| 33 |
+
ATOM 32 HZ1 LYS A 2 11.993 2.245 -4.410 1.00 0.00 H
|
| 34 |
+
ATOM 33 HZ2 LYS A 2 13.326 1.788 -3.552 1.00 0.00 H
|
| 35 |
+
ATOM 34 HZ3 LYS A 2 11.993 0.817 -3.585 1.00 0.00 H
|
| 36 |
+
ATOM 35 C LYS A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 37 |
+
ATOM 36 O LYS A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 38 |
+
ATOM 37 OXT LYS A 2 9.441 5.327 0.055 1.00 0.00 O
|
| 39 |
+
TER 38 LYS A 2
|
| 40 |
+
ENDMDL
|
| 41 |
+
END
|
2AA-complete/test/DL-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:2380d3a4fc93dca97e36c0037db7a865f84f2b9e5a1a5e5ebb9328309553f03f
|
| 3 |
+
size 12310296
|
2AA-complete/test/DL-traj-state0.pdb
ADDED
|
@@ -0,0 +1,38 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
MODEL 0
|
| 2 |
+
ATOM 1 N ASP A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ASP A 1 2.495 1.310 0.838 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ASP A 1 2.638 1.448 -0.985 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ASP A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ASP A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ASP A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ASP A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB2 ASP A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB3 ASP A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 11 |
+
ATOM 10 CG ASP A 1 4.275 5.011 1.195 1.00 0.00 C
|
| 12 |
+
ATOM 11 OD1 ASP A 1 3.669 5.955 0.620 1.00 0.00 O
|
| 13 |
+
ATOM 12 OD2 ASP A 1 5.408 5.092 1.741 1.00 0.00 O
|
| 14 |
+
ATOM 13 C ASP A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 15 |
+
ATOM 14 O ASP A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 16 |
+
ATOM 15 N LEU A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 17 |
+
ATOM 16 H LEU A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 18 |
+
ATOM 17 CA LEU A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 19 |
+
ATOM 18 HA LEU A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 20 |
+
ATOM 19 CB LEU A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 21 |
+
ATOM 20 HB2 LEU A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 22 |
+
ATOM 21 HB3 LEU A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 23 |
+
ATOM 22 CG LEU A 2 9.713 3.149 -1.195 1.00 0.00 C
|
| 24 |
+
ATOM 23 HG LEU A 2 10.062 4.181 -1.186 1.00 0.00 H
|
| 25 |
+
ATOM 24 CD1 LEU A 2 10.201 2.437 0.063 1.00 0.00 C
|
| 26 |
+
ATOM 25 HD11 LEU A 2 9.853 1.404 0.055 1.00 0.00 H
|
| 27 |
+
ATOM 26 HD12 LEU A 2 11.291 2.452 0.090 1.00 0.00 H
|
| 28 |
+
ATOM 27 HD13 LEU A 2 9.809 2.945 0.944 1.00 0.00 H
|
| 29 |
+
ATOM 28 CD2 LEU A 2 10.262 2.438 -2.427 1.00 0.00 C
|
| 30 |
+
ATOM 29 HD21 LEU A 2 9.914 2.946 -3.326 1.00 0.00 H
|
| 31 |
+
ATOM 30 HD22 LEU A 2 11.352 2.453 -2.400 1.00 0.00 H
|
| 32 |
+
ATOM 31 HD23 LEU A 2 9.914 1.405 -2.436 1.00 0.00 H
|
| 33 |
+
ATOM 32 C LEU A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 34 |
+
ATOM 33 O LEU A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 35 |
+
ATOM 34 OXT LEU A 2 9.440 5.339 0.048 1.00 0.00 O
|
| 36 |
+
TER 35 LEU A 2
|
| 37 |
+
ENDMDL
|
| 38 |
+
END
|
2AA-complete/test/DW-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:f46d5021078f994a313df08158b235b39f652af04d3ba13abd3c0b45bcd2deea
|
| 3 |
+
size 14074296
|
2AA-complete/test/DW-traj-state0.pdb
ADDED
|
@@ -0,0 +1,43 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
MODEL 0
|
| 2 |
+
ATOM 1 N ASP A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 ASP A 1 2.643 1.451 -0.988 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 ASP A 1 2.496 1.307 0.838 1.00 0.00 H
|
| 5 |
+
ATOM 4 H ASP A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA ASP A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA ASP A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB ASP A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB2 ASP A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB3 ASP A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 11 |
+
ATOM 10 CG ASP A 1 4.275 5.011 1.195 1.00 0.00 C
|
| 12 |
+
ATOM 11 OD1 ASP A 1 3.669 5.955 0.620 1.00 0.00 O
|
| 13 |
+
ATOM 12 OD2 ASP A 1 5.408 5.092 1.741 1.00 0.00 O
|
| 14 |
+
ATOM 13 C ASP A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 15 |
+
ATOM 14 O ASP A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 16 |
+
ATOM 15 N TRP A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 17 |
+
ATOM 16 H TRP A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 18 |
+
ATOM 17 CA TRP A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 19 |
+
ATOM 18 HA TRP A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 20 |
+
ATOM 19 CB TRP A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 21 |
+
ATOM 20 HB2 TRP A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 22 |
+
ATOM 21 HB3 TRP A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 23 |
+
ATOM 22 CG TRP A 2 9.696 3.076 -1.321 1.00 0.00 C
|
| 24 |
+
ATOM 23 CD1 TRP A 2 10.427 2.515 -2.293 1.00 0.00 C
|
| 25 |
+
ATOM 24 HD1 TRP A 2 9.934 2.029 -3.135 1.00 0.00 H
|
| 26 |
+
ATOM 25 NE1 TRP A 2 11.801 2.713 -1.950 1.00 0.00 N
|
| 27 |
+
ATOM 26 HE1 TRP A 2 12.593 2.399 -2.493 1.00 0.00 H
|
| 28 |
+
ATOM 27 CE2 TRP A 2 11.867 3.367 -0.817 1.00 0.00 C
|
| 29 |
+
ATOM 28 CZ2 TRP A 2 13.013 3.770 -0.120 1.00 0.00 C
|
| 30 |
+
ATOM 29 HZ2 TRP A 2 14.002 3.540 -0.517 1.00 0.00 H
|
| 31 |
+
ATOM 30 CH2 TRP A 2 12.793 4.456 1.069 1.00 0.00 C
|
| 32 |
+
ATOM 31 HH2 TRP A 2 13.639 4.799 1.664 1.00 0.00 H
|
| 33 |
+
ATOM 32 CZ3 TRP A 2 11.540 4.708 1.505 1.00 0.00 C
|
| 34 |
+
ATOM 33 HZ3 TRP A 2 11.387 5.247 2.440 1.00 0.00 H
|
| 35 |
+
ATOM 34 CE3 TRP A 2 10.401 4.292 0.786 1.00 0.00 C
|
| 36 |
+
ATOM 35 HE3 TRP A 2 9.405 4.513 1.168 1.00 0.00 H
|
| 37 |
+
ATOM 36 CD2 TRP A 2 10.623 3.601 -0.412 1.00 0.00 C
|
| 38 |
+
ATOM 37 C TRP A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 39 |
+
ATOM 38 O TRP A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 40 |
+
ATOM 39 OXT TRP A 2 9.436 5.333 0.022 1.00 0.00 O
|
| 41 |
+
TER 40 TRP A 2
|
| 42 |
+
ENDMDL
|
| 43 |
+
END
|
2AA-complete/test/EK-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:4f893591f10202e7f29e2ddc4a4b251b4bc820cc0394eabec616928e722a98ff
|
| 3 |
+
size 14427096
|
2AA-complete/test/EK-traj-state0.pdb
ADDED
|
@@ -0,0 +1,44 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
MODEL 0
|
| 2 |
+
ATOM 1 N GLU A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 GLU A 1 2.641 1.438 -0.986 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 GLU A 1 2.499 1.306 0.842 1.00 0.00 H
|
| 5 |
+
ATOM 4 H GLU A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA GLU A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA GLU A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB GLU A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB2 GLU A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB3 GLU A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 11 |
+
ATOM 10 CG GLU A 1 4.267 4.996 1.195 1.00 0.00 C
|
| 12 |
+
ATOM 11 HG2 GLU A 1 5.347 4.850 1.186 1.00 0.00 H
|
| 13 |
+
ATOM 12 HG3 GLU A 1 3.967 5.535 0.296 1.00 0.00 H
|
| 14 |
+
ATOM 13 CD GLU A 1 3.874 5.805 2.429 1.00 0.00 C
|
| 15 |
+
ATOM 14 OE1 GLU A 1 4.595 5.679 3.454 1.00 0.00 O
|
| 16 |
+
ATOM 15 OE2 GLU A 1 2.856 6.542 2.334 1.00 0.00 O
|
| 17 |
+
ATOM 16 C GLU A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 18 |
+
ATOM 17 O GLU A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 19 |
+
ATOM 18 N LYS A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 20 |
+
ATOM 19 H LYS A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 21 |
+
ATOM 20 CA LYS A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 22 |
+
ATOM 21 HA LYS A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 23 |
+
ATOM 22 CB LYS A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 24 |
+
ATOM 23 HB2 LYS A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 25 |
+
ATOM 24 HB3 LYS A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 26 |
+
ATOM 25 CG LYS A 2 9.713 3.149 -1.195 1.00 0.00 C
|
| 27 |
+
ATOM 26 HG2 LYS A 2 10.062 4.181 -1.186 1.00 0.00 H
|
| 28 |
+
ATOM 27 HG3 LYS A 2 10.062 2.640 -0.296 1.00 0.00 H
|
| 29 |
+
ATOM 28 CD LYS A 2 10.262 2.438 -2.427 1.00 0.00 C
|
| 30 |
+
ATOM 29 HD2 LYS A 2 9.914 1.405 -2.436 1.00 0.00 H
|
| 31 |
+
ATOM 30 HD3 LYS A 2 9.914 2.946 -3.326 1.00 0.00 H
|
| 32 |
+
ATOM 31 CE LYS A 2 11.787 2.459 -2.389 1.00 0.00 C
|
| 33 |
+
ATOM 32 HE2 LYS A 2 12.136 3.492 -2.380 1.00 0.00 H
|
| 34 |
+
ATOM 33 HE3 LYS A 2 12.136 1.951 -1.491 1.00 0.00 H
|
| 35 |
+
ATOM 34 NZ LYS A 2 12.316 1.773 -3.577 1.00 0.00 N
|
| 36 |
+
ATOM 35 HZ1 LYS A 2 11.993 2.245 -4.410 1.00 0.00 H
|
| 37 |
+
ATOM 36 HZ2 LYS A 2 13.326 1.788 -3.552 1.00 0.00 H
|
| 38 |
+
ATOM 37 HZ3 LYS A 2 11.993 0.817 -3.585 1.00 0.00 H
|
| 39 |
+
ATOM 38 C LYS A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 40 |
+
ATOM 39 O LYS A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 41 |
+
ATOM 40 OXT LYS A 2 9.440 5.325 0.059 1.00 0.00 O
|
| 42 |
+
TER 41 LYS A 2
|
| 43 |
+
ENDMDL
|
| 44 |
+
END
|
2AA-complete/test/EL-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:dc6ee44f31b013e5ba205abd1f5d81b762e6234dbb6b24c925fa6249d1c612b7
|
| 3 |
+
size 13368696
|
2AA-complete/test/EL-traj-state0.pdb
ADDED
|
@@ -0,0 +1,41 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
MODEL 0
|
| 2 |
+
ATOM 1 N GLU A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 GLU A 1 2.493 1.309 0.836 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 GLU A 1 2.641 1.444 -0.986 1.00 0.00 H
|
| 5 |
+
ATOM 4 H GLU A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA GLU A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA GLU A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB GLU A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB2 GLU A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB3 GLU A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 11 |
+
ATOM 10 CG GLU A 1 4.267 4.996 1.195 1.00 0.00 C
|
| 12 |
+
ATOM 11 HG2 GLU A 1 5.347 4.850 1.186 1.00 0.00 H
|
| 13 |
+
ATOM 12 HG3 GLU A 1 3.967 5.535 0.296 1.00 0.00 H
|
| 14 |
+
ATOM 13 CD GLU A 1 3.874 5.805 2.429 1.00 0.00 C
|
| 15 |
+
ATOM 14 OE1 GLU A 1 4.595 5.679 3.454 1.00 0.00 O
|
| 16 |
+
ATOM 15 OE2 GLU A 1 2.856 6.542 2.334 1.00 0.00 O
|
| 17 |
+
ATOM 16 C GLU A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 18 |
+
ATOM 17 O GLU A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 19 |
+
ATOM 18 N LEU A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 20 |
+
ATOM 19 H LEU A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 21 |
+
ATOM 20 CA LEU A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 22 |
+
ATOM 21 HA LEU A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 23 |
+
ATOM 22 CB LEU A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 24 |
+
ATOM 23 HB2 LEU A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 25 |
+
ATOM 24 HB3 LEU A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 26 |
+
ATOM 25 CG LEU A 2 9.713 3.149 -1.195 1.00 0.00 C
|
| 27 |
+
ATOM 26 HG LEU A 2 10.062 4.181 -1.186 1.00 0.00 H
|
| 28 |
+
ATOM 27 CD1 LEU A 2 10.201 2.437 0.063 1.00 0.00 C
|
| 29 |
+
ATOM 28 HD11 LEU A 2 9.853 1.404 0.055 1.00 0.00 H
|
| 30 |
+
ATOM 29 HD12 LEU A 2 11.291 2.452 0.090 1.00 0.00 H
|
| 31 |
+
ATOM 30 HD13 LEU A 2 9.809 2.945 0.944 1.00 0.00 H
|
| 32 |
+
ATOM 31 CD2 LEU A 2 10.262 2.438 -2.427 1.00 0.00 C
|
| 33 |
+
ATOM 32 HD21 LEU A 2 9.914 2.946 -3.326 1.00 0.00 H
|
| 34 |
+
ATOM 33 HD22 LEU A 2 11.352 2.453 -2.400 1.00 0.00 H
|
| 35 |
+
ATOM 34 HD23 LEU A 2 9.914 1.405 -2.436 1.00 0.00 H
|
| 36 |
+
ATOM 35 C LEU A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 37 |
+
ATOM 36 O LEU A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 38 |
+
ATOM 37 OXT LEU A 2 9.440 5.337 0.052 1.00 0.00 O
|
| 39 |
+
TER 38 LEU A 2
|
| 40 |
+
ENDMDL
|
| 41 |
+
END
|
2AA-complete/test/ET-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:85f501b8f18a510fbd9ef52e25f4772a3cecdeea41bc05a4e1ddbc74bf08be15
|
| 3 |
+
size 11604696
|
2AA-complete/test/ET-traj-state0.pdb
ADDED
|
@@ -0,0 +1,36 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
MODEL 0
|
| 2 |
+
ATOM 1 N GLU A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 GLU A 1 2.497 1.306 0.839 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 GLU A 1 2.633 1.445 -0.981 1.00 0.00 H
|
| 5 |
+
ATOM 4 H GLU A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA GLU A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA GLU A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB GLU A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB2 GLU A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB3 GLU A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 11 |
+
ATOM 10 CG GLU A 1 4.267 4.996 1.195 1.00 0.00 C
|
| 12 |
+
ATOM 11 HG2 GLU A 1 5.347 4.850 1.186 1.00 0.00 H
|
| 13 |
+
ATOM 12 HG3 GLU A 1 3.967 5.535 0.296 1.00 0.00 H
|
| 14 |
+
ATOM 13 CD GLU A 1 3.874 5.805 2.429 1.00 0.00 C
|
| 15 |
+
ATOM 14 OE1 GLU A 1 4.595 5.679 3.454 1.00 0.00 O
|
| 16 |
+
ATOM 15 OE2 GLU A 1 2.856 6.542 2.334 1.00 0.00 O
|
| 17 |
+
ATOM 16 C GLU A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 18 |
+
ATOM 17 O GLU A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 19 |
+
ATOM 18 N THR A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 20 |
+
ATOM 19 H THR A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 21 |
+
ATOM 20 CA THR A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 22 |
+
ATOM 21 HA THR A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 23 |
+
ATOM 22 CB THR A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 24 |
+
ATOM 23 HB THR A 2 9.279 3.142 -1.206 1.00 0.00 H
|
| 25 |
+
ATOM 24 CG2 THR A 2 7.701 1.682 -1.244 1.00 0.00 C
|
| 26 |
+
ATOM 25 HG21 THR A 2 6.612 1.666 -1.271 1.00 0.00 H
|
| 27 |
+
ATOM 26 HG22 THR A 2 8.093 1.173 -2.125 1.00 0.00 H
|
| 28 |
+
ATOM 27 HG23 THR A 2 8.050 1.173 -0.346 1.00 0.00 H
|
| 29 |
+
ATOM 28 OG1 THR A 2 7.732 3.795 -2.411 1.00 0.00 O
|
| 30 |
+
ATOM 29 HG1 THR A 2 8.077 3.347 -3.187 1.00 0.00 H
|
| 31 |
+
ATOM 30 C THR A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 32 |
+
ATOM 31 O THR A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 33 |
+
ATOM 32 OXT THR A 2 9.443 5.319 0.030 1.00 0.00 O
|
| 34 |
+
TER 33 THR A 2
|
| 35 |
+
ENDMDL
|
| 36 |
+
END
|
2AA-complete/test/EV-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:5102ea306a323815ec3aed35f26690a9a8b5e099e9ae61c331caa5f1f60d494c
|
| 3 |
+
size 12310296
|
2AA-complete/test/EV-traj-state0.pdb
ADDED
|
@@ -0,0 +1,38 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
MODEL 0
|
| 2 |
+
ATOM 1 N GLU A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 GLU A 1 2.496 1.300 0.837 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 GLU A 1 2.640 1.450 -0.986 1.00 0.00 H
|
| 5 |
+
ATOM 4 H GLU A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA GLU A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA GLU A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB GLU A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB2 GLU A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB3 GLU A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 11 |
+
ATOM 10 CG GLU A 1 4.267 4.996 1.195 1.00 0.00 C
|
| 12 |
+
ATOM 11 HG2 GLU A 1 5.347 4.850 1.186 1.00 0.00 H
|
| 13 |
+
ATOM 12 HG3 GLU A 1 3.967 5.535 0.296 1.00 0.00 H
|
| 14 |
+
ATOM 13 CD GLU A 1 3.874 5.805 2.429 1.00 0.00 C
|
| 15 |
+
ATOM 14 OE1 GLU A 1 4.595 5.679 3.454 1.00 0.00 O
|
| 16 |
+
ATOM 15 OE2 GLU A 1 2.856 6.542 2.334 1.00 0.00 O
|
| 17 |
+
ATOM 16 C GLU A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 18 |
+
ATOM 17 O GLU A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 19 |
+
ATOM 18 N VAL A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 20 |
+
ATOM 19 H VAL A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 21 |
+
ATOM 20 CA VAL A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 22 |
+
ATOM 21 HA VAL A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 23 |
+
ATOM 22 CB VAL A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 24 |
+
ATOM 23 HB VAL A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 25 |
+
ATOM 24 CG1 VAL A 2 7.701 3.839 -2.490 1.00 0.00 C
|
| 26 |
+
ATOM 25 HG11 VAL A 2 8.050 4.872 -2.481 1.00 0.00 H
|
| 27 |
+
ATOM 26 HG12 VAL A 2 8.093 3.331 -3.371 1.00 0.00 H
|
| 28 |
+
ATOM 27 HG13 VAL A 2 6.612 3.824 -2.517 1.00 0.00 H
|
| 29 |
+
ATOM 28 CG2 VAL A 2 9.713 3.149 -1.195 1.00 0.00 C
|
| 30 |
+
ATOM 29 HG21 VAL A 2 10.062 2.640 -0.296 1.00 0.00 H
|
| 31 |
+
ATOM 30 HG22 VAL A 2 10.106 2.641 -2.075 1.00 0.00 H
|
| 32 |
+
ATOM 31 HG23 VAL A 2 10.062 4.181 -1.186 1.00 0.00 H
|
| 33 |
+
ATOM 32 C VAL A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 34 |
+
ATOM 33 O VAL A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 35 |
+
ATOM 34 OXT VAL A 2 9.441 5.326 0.059 1.00 0.00 O
|
| 36 |
+
TER 35 VAL A 2
|
| 37 |
+
ENDMDL
|
| 38 |
+
END
|
2AA-complete/test/EW-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:08880b44d6b01618de6004ccf9a3aa9ebc2d354fa267d2b7414da53ed312e250
|
| 3 |
+
size 15132696
|
2AA-complete/test/EW-traj-state0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
MODEL 0
|
| 2 |
+
ATOM 1 N GLU A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 GLU A 1 2.648 1.442 -0.991 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 GLU A 1 2.490 1.307 0.833 1.00 0.00 H
|
| 5 |
+
ATOM 4 H GLU A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA GLU A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA GLU A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB GLU A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB2 GLU A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB3 GLU A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 11 |
+
ATOM 10 CG GLU A 1 4.267 4.996 1.195 1.00 0.00 C
|
| 12 |
+
ATOM 11 HG2 GLU A 1 5.347 4.850 1.186 1.00 0.00 H
|
| 13 |
+
ATOM 12 HG3 GLU A 1 3.967 5.535 0.296 1.00 0.00 H
|
| 14 |
+
ATOM 13 CD GLU A 1 3.874 5.805 2.429 1.00 0.00 C
|
| 15 |
+
ATOM 14 OE1 GLU A 1 4.595 5.679 3.454 1.00 0.00 O
|
| 16 |
+
ATOM 15 OE2 GLU A 1 2.856 6.542 2.334 1.00 0.00 O
|
| 17 |
+
ATOM 16 C GLU A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 18 |
+
ATOM 17 O GLU A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 19 |
+
ATOM 18 N TRP A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 20 |
+
ATOM 19 H TRP A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 21 |
+
ATOM 20 CA TRP A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 22 |
+
ATOM 21 HA TRP A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 23 |
+
ATOM 22 CB TRP A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 24 |
+
ATOM 23 HB2 TRP A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 25 |
+
ATOM 24 HB3 TRP A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 26 |
+
ATOM 25 CG TRP A 2 9.696 3.076 -1.321 1.00 0.00 C
|
| 27 |
+
ATOM 26 CD1 TRP A 2 10.427 2.515 -2.293 1.00 0.00 C
|
| 28 |
+
ATOM 27 HD1 TRP A 2 9.934 2.029 -3.135 1.00 0.00 H
|
| 29 |
+
ATOM 28 NE1 TRP A 2 11.801 2.713 -1.950 1.00 0.00 N
|
| 30 |
+
ATOM 29 HE1 TRP A 2 12.593 2.399 -2.493 1.00 0.00 H
|
| 31 |
+
ATOM 30 CE2 TRP A 2 11.867 3.367 -0.817 1.00 0.00 C
|
| 32 |
+
ATOM 31 CZ2 TRP A 2 13.013 3.770 -0.120 1.00 0.00 C
|
| 33 |
+
ATOM 32 HZ2 TRP A 2 14.002 3.540 -0.517 1.00 0.00 H
|
| 34 |
+
ATOM 33 CH2 TRP A 2 12.793 4.456 1.069 1.00 0.00 C
|
| 35 |
+
ATOM 34 HH2 TRP A 2 13.639 4.799 1.664 1.00 0.00 H
|
| 36 |
+
ATOM 35 CZ3 TRP A 2 11.540 4.708 1.505 1.00 0.00 C
|
| 37 |
+
ATOM 36 HZ3 TRP A 2 11.387 5.247 2.440 1.00 0.00 H
|
| 38 |
+
ATOM 37 CE3 TRP A 2 10.401 4.292 0.786 1.00 0.00 C
|
| 39 |
+
ATOM 38 HE3 TRP A 2 9.405 4.513 1.168 1.00 0.00 H
|
| 40 |
+
ATOM 39 CD2 TRP A 2 10.623 3.601 -0.412 1.00 0.00 C
|
| 41 |
+
ATOM 40 C TRP A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 42 |
+
ATOM 41 O TRP A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 43 |
+
ATOM 42 OXT TRP A 2 9.436 5.330 0.027 1.00 0.00 O
|
| 44 |
+
TER 43 TRP A 2
|
| 45 |
+
ENDMDL
|
| 46 |
+
END
|
2AA-complete/test/EY-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:3ac6123d1e8f0045ee66797aebf4b5de953d54deb427ff0af20aa484659b4bf8
|
| 3 |
+
size 14074296
|
2AA-complete/test/EY-traj-state0.pdb
ADDED
|
@@ -0,0 +1,43 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
MODEL 0
|
| 2 |
+
ATOM 1 N GLU A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 GLU A 1 2.645 1.444 -0.990 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 GLU A 1 2.491 1.305 0.834 1.00 0.00 H
|
| 5 |
+
ATOM 4 H GLU A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA GLU A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA GLU A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB GLU A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB2 GLU A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB3 GLU A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 11 |
+
ATOM 10 CG GLU A 1 4.267 4.996 1.195 1.00 0.00 C
|
| 12 |
+
ATOM 11 HG2 GLU A 1 5.347 4.850 1.186 1.00 0.00 H
|
| 13 |
+
ATOM 12 HG3 GLU A 1 3.967 5.535 0.296 1.00 0.00 H
|
| 14 |
+
ATOM 13 CD GLU A 1 3.874 5.805 2.429 1.00 0.00 C
|
| 15 |
+
ATOM 14 OE1 GLU A 1 4.595 5.679 3.454 1.00 0.00 O
|
| 16 |
+
ATOM 15 OE2 GLU A 1 2.856 6.542 2.334 1.00 0.00 O
|
| 17 |
+
ATOM 16 C GLU A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 18 |
+
ATOM 17 O GLU A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 19 |
+
ATOM 18 N TYR A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 20 |
+
ATOM 19 H TYR A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 21 |
+
ATOM 20 CA TYR A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 22 |
+
ATOM 21 HA TYR A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 23 |
+
ATOM 22 CB TYR A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 24 |
+
ATOM 23 HB2 TYR A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 25 |
+
ATOM 24 HB3 TYR A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 26 |
+
ATOM 25 CG TYR A 2 9.698 3.149 -1.195 1.00 0.00 C
|
| 27 |
+
ATOM 26 CD1 TYR A 2 10.433 2.553 -2.227 1.00 0.00 C
|
| 28 |
+
ATOM 27 HD1 TYR A 2 9.915 2.073 -3.058 1.00 0.00 H
|
| 29 |
+
ATOM 28 CE1 TYR A 2 11.832 2.573 -2.193 1.00 0.00 C
|
| 30 |
+
ATOM 29 HE1 TYR A 2 12.404 2.109 -2.997 1.00 0.00 H
|
| 31 |
+
ATOM 30 CZ TYR A 2 12.497 3.189 -1.126 1.00 0.00 C
|
| 32 |
+
ATOM 31 OH TYR A 2 13.857 3.208 -1.092 1.00 0.00 O
|
| 33 |
+
ATOM 32 HH TYR A 2 14.257 2.772 -1.848 1.00 0.00 H
|
| 34 |
+
ATOM 33 CE2 TYR A 2 11.763 3.785 -0.094 1.00 0.00 C
|
| 35 |
+
ATOM 34 HE2 TYR A 2 12.281 4.264 0.737 1.00 0.00 H
|
| 36 |
+
ATOM 35 CD2 TYR A 2 10.364 3.765 -0.128 1.00 0.00 C
|
| 37 |
+
ATOM 36 HD2 TYR A 2 9.792 4.229 0.676 1.00 0.00 H
|
| 38 |
+
ATOM 37 C TYR A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 39 |
+
ATOM 38 O TYR A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 40 |
+
ATOM 39 OXT TYR A 2 9.436 5.335 0.070 1.00 0.00 O
|
| 41 |
+
TER 40 TYR A 2
|
| 42 |
+
ENDMDL
|
| 43 |
+
END
|
2AA-complete/test/FA-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:e5ca21369228c458e11ac6a5c434b05712e1f3250c2306de6fbdd0faa59c244f
|
| 3 |
+
size 11957496
|
2AA-complete/test/FA-traj-state0.pdb
ADDED
|
@@ -0,0 +1,37 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
MODEL 0
|
| 2 |
+
ATOM 1 N PHE A 1 3.326 1.548 0.000 1.00 0.00 N
|
| 3 |
+
ATOM 2 H2 PHE A 1 2.492 1.305 0.834 1.00 0.00 H
|
| 4 |
+
ATOM 3 H3 PHE A 1 2.644 1.444 -0.988 1.00 0.00 H
|
| 5 |
+
ATOM 4 H PHE A 1 3.909 0.724 0.000 1.00 0.00 H
|
| 6 |
+
ATOM 5 CA PHE A 1 3.970 2.846 0.000 1.00 0.00 C
|
| 7 |
+
ATOM 6 HA PHE A 1 3.672 3.400 -0.890 1.00 0.00 H
|
| 8 |
+
ATOM 7 CB PHE A 1 3.577 3.654 1.232 1.00 0.00 C
|
| 9 |
+
ATOM 8 HB2 PHE A 1 2.497 3.801 1.241 1.00 0.00 H
|
| 10 |
+
ATOM 9 HB3 PHE A 1 3.877 3.116 2.131 1.00 0.00 H
|
| 11 |
+
ATOM 10 CG PHE A 1 4.201 5.026 1.321 1.00 0.00 C
|
| 12 |
+
ATOM 11 CD1 PHE A 1 3.912 5.857 2.410 1.00 0.00 C
|
| 13 |
+
ATOM 12 HD1 PHE A 1 3.236 5.514 3.193 1.00 0.00 H
|
| 14 |
+
ATOM 13 CE1 PHE A 1 4.490 7.130 2.492 1.00 0.00 C
|
| 15 |
+
ATOM 14 HE1 PHE A 1 4.265 7.777 3.340 1.00 0.00 H
|
| 16 |
+
ATOM 15 CZ PHE A 1 5.358 7.571 1.486 1.00 0.00 C
|
| 17 |
+
ATOM 16 HZ PHE A 1 5.808 8.561 1.550 1.00 0.00 H
|
| 18 |
+
ATOM 17 CE2 PHE A 1 5.647 6.739 0.397 1.00 0.00 C
|
| 19 |
+
ATOM 18 HE2 PHE A 1 6.322 7.083 -0.386 1.00 0.00 H
|
| 20 |
+
ATOM 19 CD2 PHE A 1 5.068 5.467 0.315 1.00 0.00 C
|
| 21 |
+
ATOM 20 HD2 PHE A 1 5.294 4.820 -0.533 1.00 0.00 H
|
| 22 |
+
ATOM 21 C PHE A 1 5.486 2.705 0.000 1.00 0.00 C
|
| 23 |
+
ATOM 22 O PHE A 1 6.009 1.593 0.000 1.00 0.00 O
|
| 24 |
+
ATOM 23 N ALA A 2 6.191 3.839 0.000 1.00 0.00 N
|
| 25 |
+
ATOM 24 H ALA A 2 5.715 4.730 0.000 1.00 0.00 H
|
| 26 |
+
ATOM 25 CA ALA A 2 7.640 3.839 0.000 1.00 0.00 C
|
| 27 |
+
ATOM 26 HA ALA A 2 8.004 3.325 0.890 1.00 0.00 H
|
| 28 |
+
ATOM 27 CB ALA A 2 8.189 3.127 -1.232 1.00 0.00 C
|
| 29 |
+
ATOM 28 HB1 ALA A 2 7.841 3.636 -2.131 1.00 0.00 H
|
| 30 |
+
ATOM 29 HB2 ALA A 2 9.279 3.142 -1.206 1.00 0.00 H
|
| 31 |
+
ATOM 30 HB3 ALA A 2 7.841 2.094 -1.241 1.00 0.00 H
|
| 32 |
+
ATOM 31 C ALA A 2 8.188 5.259 0.000 1.00 0.00 C
|
| 33 |
+
ATOM 32 O ALA A 2 7.425 6.222 0.000 1.00 0.00 O
|
| 34 |
+
ATOM 33 OXT ALA A 2 9.444 5.307 -0.015 1.00 0.00 O
|
| 35 |
+
TER 34 ALA A 2
|
| 36 |
+
ENDMDL
|
| 37 |
+
END
|
2AA-complete/test/FF-traj-arrays.npz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:ca04eef5eacde9f65a53d9c50937fb5e070ae2a53f1c19f71066ef08b310185b
|
| 3 |
+
size 15485496
|