DOI: 10.5061/dryad.5mkkwh7bp
title: Data from: programming co-assembled peptide nanofiber morphology via anionic amino acid type: insights from molecular dynamics simulations

description: Co-assembling peptides can be crafted into supramolecular biomaterials for
 use in biotechnological applications, such as cell culture scaffolds, drug
 delivery, biosensors, and tissue engineering. Peptide co-assembly refers
 to the spontaneous organization of two different peptides into a
 supramolecular architecture. Here we use molecular dynamics simulations to
 quantify the effect of anionic amino acid type on co-assembly dynamics and
 nanofiber structure in binary CATCH(+/-) peptide systems. CATCH peptide
 sequences follow a general pattern: CQCFCFCFCQC, where all C’s are either
 a positively charged or a negatively charged amino acid. Specifically, we
 investigate the effect of substituting aspartic acid residues for the
 glutamic acid residues in the established CATCH(6E-) molecule, while
 keeping CATCH(6K+) unchanged. Our results show that structures consisting
 of CATCH(6K+) and CATCH(6D-) form flatter β-sheets, have stronger
 interactions between charged residues on opposing β-sheet faces, and have
 slower co-assembly kinetics than structures consisting of CATCH(6K+) and
 CATCH(6E-). Knowledge of the effect of sidechain type on assembly dynamics
 and fibrillar structure can help guide the development of advanced
 biomaterials and grant insight into sequence-to-structure relationships.
description: Please refer to the manuscript for details.
 Citation: Dong X, Liu R, Seroski DT, Hudalla GA, Hall CK.
 Programming co-assembled peptide nanofiber morphology via anionic amino
 acid type: Insights from molecular dynamics simulations. <em>PLOS
 Computational Biology.</em>
description: # Dataset from Programming co-assembled peptide nanofiber morphology via
 anionic amino acid type: Insights from molecular dynamics simulations
 Dataset --- Dong X, Liu R, Seroski DT, Hudalla GA, Hall CK. Programming
 co-assembled peptide nanofiber morphology via anionic amino acid type:
 Insights from molecular dynamics simulations. *PLOS Computational
 Biology.* This directory contains the results and the analysis from
 atomistic molecular dynamics simulations (AMBER/MD) and coarse-grained
 discontinuous molecular dynamics (PRIME20/DMD) simulations for the
 investigation of amino acid type on co-assembled peptide nanofiber
 morphology. # Table of Contents 1. [General overview of data
 included](#general-overview) 2. [Description of output simulation data
 files used for analysis](#output) 3. [Description of scripts and software
 used for simulation analysis and the resulting output data analysis
 files](#scripts) * [Contact map calculation](#contact) * [DSSP (Define
 Secondary Structure of Proteins) analysis](#dssp) * [Hydrogen bonding
 analysis](#hbcalc) * [LIE (Linear interaction energy) analysis](#lie) *
 [MM/GBSA (Molecular mechanics with generalised Born and surface area
 solvation) analysis](#mmgbsa) 4. [File tree and general description of
 subdirectories and file organization for each tarball](#file-tree) *
 [annealing-catch-repo.tar.gz](#annealing-catch-repo-tree) *
 [catch-remd-repo.tar.gz](#catch-remd-repo-tree) *
 [catch-stacking-repo.tar.gz](#catch-stacking-repo-tree) *
 [CATCH.DMD.tar.gz](#catch-dmd-tree) 5. [Code/Software
 Availability](#code-software-availability) ## General overview of data
 included Coordinate
 files and analysis outputs from simulations are archived and compressed
 using tar and gzip. Files are organized in a similar structure to the
 manuscript. Parameter and topology files are included for MD simulations.
 | tarball name | description | | --------------------------- |
 --------------------------------------------------------------------------------------------- | | annealing-catch-repo.tar.gz | contains results and files relating to MD single bilayer and two stacked bilayer simulations | | catch-remd-repo.tar.gz | contains results and files relating to REMD simulations of single CATCH peptide | | catch-stacking-repo.tar.gz | contains results and files relating to MD two separated bilayer simulations | | CATCH.DMD.tar.gz | contains results and files relating to PRIME20/DMD simulations | To preview the files within each tarball use the following command: `tar -tf tarball.tar.gz`. A file tree has been created for each tarball. These can be recreated using the tree command: `tar -tf tarball.tar.gz | tree --fromfile .`. ## Description of output simulation data files used for analysis ### AMBER molecular dynamics (MD) simulations Each AMBER MD simulation produces a final coordinate file necessary for analysis. The coordinate files have a *mdcrd* file extension. For traditional MD simulations, the files are labeled *equil40.mdcrd*, signifying the 40th equilibration run, corresponding to 200 ns. For REMD (replica exchange molecular dynamics), the files are labeled *remd.310K.mdcrd* corresponding to the system at T = 310 K. Paired with each coordinate file is a parameter-topology file with a *prmtop* file extension. Both coordinate and parameter-topology files are contained in the same directory for each peptide system. ### PRIME20 discontinous molecular dynamics (DMD) simulations PRIME20/DMD simulations produce two main files used for analysis: coordinate files with a *pdb* file extensions, and data files specifying hydrogen bonding partners with a *bptnr* file extension. Coordinate files follow the standard Protein Data Bank file format. Data files regarding hydrogen bonding partners with a *bptnr* extension contain a single column of integers. The first row corresponds to the collision number, the following rows corresponds to the index of the hydrogen bonding partner. As an example, consider the following snippet: *run0509.bptnr* ``` 100 30 62 ... ``` In this data file, we are given the hydrogen bonding information for collision number 100. The 1st coarse-grained bead is hydrogen bonded to the 30th coarse-grained bead. The 2nd coarse-grained bead is hydrogen bonded to the 62nd coarse-grained bead, and so forth. Hydrogen bonding information is automatically calculated and outputed as part of the PRIME20/DMD software package. ## Description of scripts and software used for simulation analysis and the resulting output data analysis files Here we describe the scripts and software used to analyze the outputs of molecular dyanamics simulations. All molecular dynamics simulations are run using AMBER (Assisted Model Building with Energy Refinement) software. [CPPTRAJ](https://amberhub.chpc.utah.edu/cpptraj/) is a program within AMBER used to proccess coordinate trajectories and data files. CPPTRAJ is the main tool used to analyze our simulation outputs. Generally, the AMBER20 package was used for MD simulation and analysis. Tools and packages availaible within CPPTRAJ and AMBER are dependent on the system administrator and the installation process chosen for the AMBER package. Instructions for installing AMBER is beyond the scope of this README file. Each analysis/calculation is done independently of one another. As such, a general workflow for each analysis can be described as follows: 1. Data Preparation - i.e. running the desired simulation 2. Running CPPTRAJ or MM/GBSA 3. Results 4. Interpretation For ease of reading and comprehension, the following subsections are organized as follows: * **subtitle** describing calcuation or analyis * a manual page link for commands used, provided as a reference for the user's curiosity, and to properly cite where variable descriptions are quoted from * a generic example of an *input script* used for calculation * command used to submit a script * an example and description of the resulting output file Ellipses `...` are used to indicate that a section of text has been omitted for conciseness. ### Contact map calculation [nativecontacts manual page](https://amberhub.chpc.utah.edu/nativecontacts/)\ **input**: *contacts.in* ``` parm 6K6D-01/6K6D.prmtop # loading parameter-topology file trajin 6K6D-01/equil40.mdcrd # loading coordinate file nativecontacts name 6K6D-01 !(:NME,ACE,WAT) byresidue # calling nativecontacts run # running command ``` The nativecontacts command has the following syntax: ``` nativecontacts [name ] [] [byresidue] ``` where:\ `[name ]` Data set name.\ `` First mask to calculate contacts for.\ `[byresidue]` Write out the contact map by residue instead of by atom. ``` cpptraj &lt; contacts.in ``` **output**: *native.6K6D-01*, *nonnative.6K6D-01* for native and nonnative contacts, respectively ``` #Residue Residue Contacts 2.000 2.000 0.0000 3.000 2.000 23.5760 4.000 2.000 15.1536 5.000 2.000 68.7520 6.000 2.000 1.0392 7.000 2.000 0.0608 8.000 2.000 0.0000 9.000 2.000 0.0000 10.000 2.000 0.0000 ``` Where the first two columns are the first and second residue number, and Contacts is the total number of contacts involved with the residue pair. ### DSSP (Define Secondary Structure of Proteins) analysis [secstruct manual page](https://amberhub.chpc.utah.edu/secstruct/)\ **input**: *sec.in* ``` parm 6D.prmtop # loading parameter-topology file trajin remd.310K.mdcrd # loading coordinate file secstruct dssp out dssp.out # calling secstruct command run # running command ``` The secstruct command has the following syntax: ``` secstruct [name ] [out ] ``` where:\ `[name ]` Data set name.\ `[out ]` Output file name for secondary structure vs time. ``` cpptraj &lt; sec.in ``` **output**: *dssp.out.sum* ``` #Residue Extended Bridge 3-10 Alpha Pi Turn Bend 1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 2 0.0000 0.0008 0.1359 0.0627 0.0000 0.1930 0.0000 3 0.0001 0.0003 0.1987 0.1758 0.0001 0.2521 0.0000 4 0.0000 0.0002 0.2674 0.2691 0.0002 0.2407 0.0978 5 0.0000 0.0010 0.2312 0.3669 0.0003 0.2470 0.0895 6 0.0001 0.0003 0.2033 0.4286 0.0004 0.2069 0.0851 7 0.0001 0.0003 0.1797 0.4604 0.0005 0.2190 0.0901 8 0.0000 0.0003 0.1653 0.4666 0.0005 0.2095 0.0682 9 0.0000 0.0001 0.1695 0.4298 0.0004 0.2475 0.1008 10 0.0001 0.0001 0.1689 0.3286 0.0003 0.2957 0.0911 11 0.0001 0.0008 0.1297 0.2081 0.0002 0.3507 0.0000 12 0.0001 0.0006 0.0722 0.1153 0.0001 0.2881 0.0000 13 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 ``` Where #Residue is the residue number, Extended is the total fraction of extended structure vs time, Bridge is the total fraction of bridge structure vs time, and so forth. ### Hydrogen bonding analysis [hbond manual page](https://amberhub.chpc.utah.edu/hbond/)\ [avg manual page](https://amberhub.chpc.utah.edu/avg/)\ **input**: *hbond_calc.in* ``` parm 6K6E-01/6K6E.prmtop # loading parameter-topology file trajin 6K6E-01/equil40.mdcrd # loading coordinate file hbond 6K6E-01 donormask :157-468&:LYS acceptormask :157-468&:GLU,ASP nointramol # calling hbond command run # running command avg 6K6E-01[UU] out hb_avg_summary.out # calculating average of 6K6E-01[UU] dataset and writing average to hb_avg_summary.out ``` The hbond command has the following syntax: ``` hbond [name ] [donormask [acceptormask ] [nointramol] ``` where:\ `[name ]` Data set name.\ `[donormask ]` Use atoms in `` as solute donor heavy atoms.\ `[acceptormask ]` Use atoms in `` as solute acceptor atoms.\ `[nointramol]` Ignore intramolecular hydrogen bonds. ``` cpptraj &lt; hbond_calc.in ``` **output**: *hb_avg_summary.out* ``` #Set [avg] [sd] [ymin] [ymax] [yminidx] [ymaxidx] [names] 1 133.4 7.493 111 156 814 1046 "6K6E-01[UU]" ``` where:\ `[avg]` Average of each set.\ `[sd]` Standard deviation of each set.\ `[ymin]` Y minimum of each set.\ `[ymax]` Y maximum of each set.\ `[yminidx]` Index of minimum Y value.\ `[ymaxidx]` Index of maximum Y value.\ `[names]` Name of each set. For salt bridge calculations, the hbond command is also used, and the results are written to the file *sb_avg_summary.out*. ### LIE (Linear interaction energy) analysis [lie manual page](https://amberhub.chpc.utah.edu/lie/)\ **input**: *lie.in* ``` parm 6K6D-01/6K6D.prmtop # loading parameter-topology file trajin 6K6D-01/equil40.mdcrd # loading coordinate file lie 6K6D-01 :LYS&!(@CA,C,O,N,H) :ASP&!(@CA,C,O,N,H) out 6K6D-01alie.out run avg 6K6D-01[EVDW] out lie_avg.out ``` The lie command has the following syntax: ``` lie [] [out ] ``` where:\ `` Data set name.\ `` Use atoms in `` as ligand atoms.\ `` Use atoms in `` as receptor atoms. ``` cpptraj &lt; lie.in ``` **output**: *6K6D-01alie.out* ``` #Frame [EELEC] [EVDW] 1 -1784.8048 -35.2083 2 -1731.6592 -61.9032 3 -1702.1564 -64.1674 4 -1570.4323 -73.3063 5 -1627.9084 -53.4717 6 -1641.7948 -66.5225 7 -1670.8649 -64.5885 8 -1740.3879 -51.1118 9 -1811.9532 -51.9266 ... ``` Where #Frame is the frame number, [EELEC] is the electrostatic energy (kcal/mol), and [EVDW] is the van der Waals energy (kcal/mol). ### MM/GBSA (Molecular mechanics with generalised Born and surface area solvation) analysis [MM/GBSA tutorial](https://ambermd.org/tutorials/advanced/tutorial3/)\ **input**: *mmgbsa.in*, *pep.prmtop*, *pep_nowater.prmtop*, *rec.prmtop*, *lig.prmtop* where:\ *pep.prmtop* is the solvated complex parameter-topology file.\ *pep_nowater.prmtop* is the complex parameter-topology file.\ *rec.prmtop* is the receptor parameter-topology file.\ *lig.prmtop* is the ligand parameter-topology file. *mmgbsa.in* ``` &general endframe=1250 / &gb igb=2, saltcon=0.00 / ``` This input file is divided into two sections: general and gb. The 'endframe' variable sets which frame of the mdcrd to stop on. The presence of the '&gb' lets the script know to perform MM-GBSA calculations with the given input values. Where `igb=2` specifies the Generalized Born method used and `saltcon=0.00` specifies the salt concentration of the system. Calling the *MMPBSA.py* provided in the AMBER package: ``` $AMBERHOME/bin/MMPBSA.py -O -i mmgbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp pep.prmtop -cp pep_nowater.prmtop -rp rec.prmtop -lp lig.prmtop -y equil40.mdcrd ``` **output**: *FINAL_RESULTS_MMPBSA.dat* ``` ... Differences (Complex - Receptor - Ligand): Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS -242.4318 17.1318 1.0835 EEL -2110.0628 479.1307 30.3029 ... ``` Where VDWAALS is van der Waals contribution from MM and EEL is the electrostatic energy as calculated by the MM force field. ## File tree and general description of subdirectories and file organization for each tarball Calculations and analysis are done using scripts from the AMBER package as previously described. Please refer to the [AMBER manual](https://ambermd.org/doc12/Amber20.pdf) for more details. In the descriptions the "*" is used as a wildcard character to be interpreted as a possible string of characters. ### annealing-catch-repo.tar.gz The **annealing-catch-repo.tar.gz** tarball contains files pertaining to atomistic MD simulations (using the AMBER forcefield) of single bilayer and two stacked bilayer structures of CATCH peptides. Each simulation had an annealing stage prior to equilibration. The directory *annealing-catchff14SB* contains the subdirectories *n12L2* and *n12L4* which correspond to the single bilayer result files and stacked bilayer result files, respectively. The subdirectory *structures* contains the starting structures for each simulation. Within *n12L2* and *n12L4* are subdirectories that are labeled systematically based on the CATCH system and the simulation run number, for example "4K4D-01" refers to the CATCH(4K+/4D-) system and is the 1st in a triplicate of simulations. Each directory that is labeled by a CATCH system name contains generally the following: the topology file (.prmtop extension), the input coordinates (.rst7 extension), along with the final simulation coordinates (equil*.mdcrd and equil*.pdb). For more information regarding these files, please refer to the [AMBER manual](https://ambermd.org/doc12/Amber20.pdf). Within *n12L2* are subdirectories regarding analysis of the results. *n12L2analysis* contains outputs from MMGBSA (*FINAL_RESULTS_MMPBSA.dat), LIE analysis (*lie.out), results for calculating the number of salt bridges (sb), and results for calculating the number of backbone (bb) and intramolecular (intra) hydrogen bonds (hb). The *n12L2contacts* directory contains results for calculating the number of native and nonnative contacts within each simulation system. Within *n12L4* are subdirectories regarding analysis of the results. The *n12L4/hb_analysis* contains results for calculating the number of hydrogen bonds. The *n12L4/contacts* directory contains results for calculating the number of native and nonnative contacts within each simulation system. The *n12L4/results* directy contains results of MMGBSA analysis. The *n12L4/sb_analysis* contains results of calculating the number of salt bridges within a system. Inputs for MMGBSA and LIE analysis can be found in the *n12L2* and *n12L4* and are labeled *mmgbsa.in* and *lie.in*, respectively. ``` . └── annealing-catchff14SB ├── n12L2 │ ├── 4K4D-01 │ │ ├── 4K4D.prmtop │ │ ├── 4K4D.rst7 │ │ ├── 4K4D_nowater.prmtop │ │ ├── 4K4D_nowater.rst7 │ │ ├── CATCH4K4Dn24.inp │ │ ├── CATCH4K4Dn24.pdb │ │ ├── equil40.mdcrd │ │ ├── equil40.pdb │ ├── 4K4D-02 │ │ ├── 4K4D.prmtop │ │ ├── 4K4D.rst7 │ │ ├── 4K4D_nowater.prmtop │ │ ├── 4K4D_nowater.rst7 │ │ ├── CATCH4K4Dn24.inp │ │ ├── CATCH4K4Dn24.pdb │ │ ├── equil40.mdcrd │ │ ├── equil40.pdb │ ├── 4K4D-03 │ │ ├── 4K4D.prmtop │ │ ├── 4K4D.rst7 │ │ ├── 4K4D_nowater.prmtop │ │ ├── 4K4D_nowater.rst7 │ │ ├── CATCH4K4Dn24.inp │ │ ├── CATCH4K4Dn24.pdb │ │ ├── equil40.mdcrd │ │ ├── equil40.pdb │ ├── 4K4E-01 │ │ ├── 4K4E.prmtop │ │ ├── 4K4E.rst7 │ │ ├── 4K4E_nowater.prmtop │ │ ├── 4K4E_nowater.rst7 │ │ ├── CATCH4K4En24.inp │ │ ├── CATCH4K4En24.pdb │ │ ├── equil40.mdcrd │ │ ├── equil40.pdb │ ├── 4K4E-02 │ │ ├── 4K4E.prmtop │ │ ├── 4K4E.rst7 │ │ ├── 4K4E_nowater.prmtop │ │ ├── 4K4E_nowater.rst7 │ │ ├── CATCH4K4En24.inp │ │ ├── CATCH4K4En24.pdb │ │ ├── equil40.mdcrd │ │ ├── equil40.pdb │ ├── 4K4E-03 │ │ ├── 4K4E.prmtop │ │ ├── 4K4E.rst7 │ │ ├── 4K4E_nowater.prmtop │ │ ├── 4K4E_nowater.rst7 │ │ ├── CATCH4K4En24.inp │ │ ├── CATCH4K4En24.pdb │ │ ├── equil40.mdcrd │ │ ├── equil40.pdb │ ├── 6K6D-01 │ │ ├── 6K6D-01.out │ │ ├── 6K6D.prmtop │ │ ├── 6K6D.rst7 │ │ ├── 6K6D_nowater.prmtop │ │ ├── 6K6D_nowater.rst7 │ │ ├── CATCH6K6Dn24.inp │ │ ├── CATCH6K6Dn24.pdb │ │ ├── equil40.mdcrd │ │ ├── lig.prmtop │ │ ├── mmgbsa.in │ │ ├── mmgbsa_script.in │ │ ├── rec.prmtop │ ├── 6K6D-02 │ │ ├── 6K6D-02.out │ │ ├── 6K6D.prmtop │ │ ├── 6K6D.rst7 │ │ ├── 6K6D_nowater.prmtop │ │ ├── 6K6D_nowater.rst7 │ │ ├── CATCH6K6Dn24.inp │ │ ├── CATCH6K6Dn24.pdb │ │ ├── equil40.mdcrd │ │ ├── equil40.pdb │ │ ├── lig.prmtop │ │ ├── mmgbsa.in │ │ ├── mmgbsa_script.in │ │ ├── rec.prmtop │ ├── 6K6D-03 │ │ ├── 6K6D-03.out │ │ ├── 6K6D.prmtop │ │ ├── 6K6D.rst7 │ │ ├── 6K6D_nowater.prmtop │ │ ├── 6K6D_nowater.rst7 │ │ ├── CATCH6K6Dn24.inp │ │ ├── CATCH6K6Dn24.pdb │ │ ├── equil40.mdcrd │ │ ├── equil40.pdb │ │ ├── lig.prmtop │ │ ├── mmgbsa.in │ │ ├── mmgbsa_script.in │ │ ├── rec.prmtop │ ├── 6K6E-01 │ │ ├── 6K6E-01.out │ │ ├── 6K6E.prmtop │ │ ├── 6K6E.rst7 │ │ ├── 6K6E_nowater.prmtop │ │ ├── 6K6E_nowater.rst7 │ │ ├── CATCH6K6En24.inp │ │ ├── CATCH6K6En24.pdb │ │ ├── equil40.mdcrd │ │ ├── lig.prmtop │ │ ├── mmgbsa.in │ │ ├── mmgbsa_script.in │ │ ├── rec.prmtop │ ├── 6K6E-02 │ │ ├── 6K6E-02.out │ │ ├── 6K6E.prmtop │ │ ├── 6K6E.rst7 │ │ ├── 6K6E_nowater.prmtop │ │ ├── 6K6E_nowater.rst7 │ │ ├── CATCH6K6En24.inp │ │ ├── CATCH6K6En24.pdb │ │ ├── equil40.mdcrd │ │ ├── equil40.pdb │ │ ├── lig.prmtop │ │ ├── mmgbsa.in │ │ ├── mmgbsa_script.in │ │ ├── rec.prmtop │ ├── 6K6E-03 │ │ ├── 6K6E-03.out │ │ ├── 6K6E.prmtop │ │ ├── 6K6E.rst7 │ │ ├── 6K6E_nowater.prmtop │ │ ├── 6K6E_nowater.rst7 │ │ ├── CATCH6K6En24.inp │ │ ├── CATCH6K6En24.pdb │ │ ├── equil40.mdcrd │ │ ├── equil40.pdb │ │ ├── lig.prmtop │ │ ├── mmgbsa.in │ │ ├── mmgbsa_script.in │ │ ├── rec.prmtop │ ├── 6K6Econtacts.in │ ├── bb_hb_calc.in │ ├── cpptraj.log │ ├── intra_hb_calc.in │ ├── lie.in │ ├── mmgbsa.in │ ├── mmgbsa_script.in │ ├── n12L2analysis │ │ ├── 6K6D-01alie.out │ │ ├── 6K6D-02alie.out │ │ ├── 6K6D-03alie.out │ │ ├── 6K6E-01alie.out │ │ ├── 6K6E-02alie.out │ │ ├── 6K6E-03alie.out │ │ ├── lie_avg.out │ │ ├── n12L2_bb_avg.out │ │ ├── n12L2_intra_hb.out │ │ └── n12L2_sb_avg.out │ ├── n12L2contacts │ │ ├── 6K6D-01equil40.pdb │ │ ├── 6K6E-01equil40.pdb │ │ ├── 6K6Econtacts.in │ │ ├── contacts.in │ │ ├── native.6K6D-01 │ │ ├── native.6K6D-02 │ │ ├── native.6K6D-03 │ │ ├── native.6K6E-01 │ │ ├── native.6K6E-02 │ │ ├── native.6K6E-03 │ │ ├── nonnative.6K6D-01 │ │ ├── nonnative.6K6D-02 │ │ ├── nonnative.6K6D-03 │ │ ├── nonnative.6K6E-01 │ │ ├── nonnative.6K6E-02 │ │ └── nonnative.6K6E-03 │ ├── nohup.out │ ├── nohup2.out │ └── salt_bridge_calc.in ├── n12L4 │ ├── 4K4D-01 │ │ ├── 4K4D.prmtop │ │ ├── 4K4D.rst7 │ │ ├── 4K4D_nowater.prmtop │ │ ├── 4K4D_nowater.rst7 │ │ ├── CATCH4K4Dn48.pdb │ │ ├── FINAL_RESULTS_MMPBSA.dat │ │ ├── equil40.mdcrd │ │ ├── equil40.pdb │ │ ├── lig.prmtop │ │ ├── mmgbsa.in │ │ ├── mmgbsa_script.in │ │ ├── rec.prmtop │ ├── 4K4D-02 │ │ ├── 4K4D.prmtop │ │ ├── 4K4D.rst7 │ │ ├── 4K4D_nowater.prmtop │ │ ├── 4K4D_nowater.rst7 │ │ ├── CATCH4K4Dn48.pdb │ │ ├── FINAL_RESULTS_MMPBSA.dat │ │ ├── equil40.mdcrd │ │ ├── equil40.pdb │ │ ├── lig.prmtop │ │ ├── mmgbsa.in │ │ ├── mmgbsa_script.in │ │ ├── rec.prmtop │ ├── 4K4D-03 │ │ ├── 4K4D.prmtop │ │ ├── 4K4D.rst7 │ │ ├── 4K4D_nowater.prmtop │ │ ├── 4K4D_nowater.rst7 │ │ ├── CATCH4K4Dn48.pdb │ │ ├── FINAL_RESULTS_MMPBSA.dat │ │ ├── equil40.mdcrd │ │ ├── equil40.pdb │ │ ├── lig.prmtop │ │ ├── mmgbsa.in │ │ ├── mmgbsa_script.in │ │ ├── rec.prmtop │ ├── 4K4E-01 │ │ ├── 4K4E.prmtop │ │ ├── 4K4E.rst7 │ │ ├── 4K4E_nowater.prmtop │ │ ├── 4K4E_nowater.rst7 │ │ ├── CATCH4K4En48.pdb │ │ ├── FINAL_RESULTS_MMPBSA.dat │ │ ├── equil40.mdcrd │ │ ├── equil40.pdb │ │ ├── lig.prmtop │ │ ├── mmgbsa.in │ │ ├── mmgbsa_script.in │ │ ├── rec.prmtop │ ├── 4K4E-02 │ │ ├── 4K4E.prmtop │ │ ├── 4K4E.rst7 │ │ ├── 4K4E_nowater.prmtop │ │ ├── 4K4E_nowater.rst7 │ │ ├── CATCH4K4En48.pdb │ │ ├── FINAL_RESULTS_MMPBSA.dat │ │ ├── equil40.mdcrd │ │ ├── equil40.pdb │ │ ├── lig.prmtop │ │ ├── mmgbsa.in │ │ ├── mmgbsa_script.in │ │ ├── rec.prmtop │ ├── 4K4E-03 │ │ ├── 4K4E.prmtop │ │ ├── 4K4E.rst7 │ │ ├── 4K4E_nowater.prmtop │ │ ├── 4K4E_nowater.rst7 │ │ ├── CATCH4K4En48.pdb │ │ ├── FINAL_RESULTS_MMPBSA.dat │ │ ├── equil40.mdcrd │ │ ├── equil40.pdb │ │ ├── lig.prmtop │ │ ├── mmgbsa.in │ │ ├── mmgbsa_script.in │ │ ├── rec.prmtop │ ├── 6K6D-01 │ │ ├── 6K6D-01.out │ │ ├── 6K6D.prmtop │ │ ├── 6K6D.rst7 │ │ ├── 6K6D_nowater.prmtop │ │ ├── 6K6D_nowater.rst7 │ │ ├── CATCH6K6Dn48.pdb │ │ ├── FINAL_RESULTS_MMPBSA.dat │ │ ├── equil40.mdcrd │ │ ├── equil40.pdb │ │ ├── lig.prmtop │ │ ├── mmgbsa.in │ │ ├── mmgbsa_run.out │ │ ├── mmgbsa_script.in │ │ ├── rec.prmtop │ ├── 6K6D-02 │ │ ├── 6K6D-02.out │ │ ├── 6K6D.prmtop │ │ ├── 6K6D.rst7 │ │ ├── 6K6D_nowater.prmtop │ │ ├── 6K6D_nowater.rst7 │ │ ├── CATCH6K6Dn48.pdb │ │ ├── FINAL_RESULTS_MMPBSA.dat │ │ ├── equil40.mdcrd │ │ ├── equil40.pdb │ │ ├── lig.prmtop │ │ ├── mmgbsa.in │ │ ├── mmgbsa_run.out │ │ ├── mmgbsa_script.in │ │ ├── rec.prmtop │ ├── 6K6D-03 │ │ ├── 6K6D-03.out │ │ ├── 6K6D.prmtop │ │ ├── 6K6D.rst7 │ │ ├── 6K6D_nowater.prmtop │ │ ├── 6K6D_nowater.rst7 │ │ ├── CATCH6K6Dn48.pdb │ │ ├── FINAL_RESULTS_MMPBSA.dat │ │ ├── equil40.mdcrd │ │ ├── equil40.pdb │ │ ├── lig.prmtop │ │ ├── mmgbsa.in │ │ ├── mmgbsa_run.out │ │ ├── mmgbsa_script.in │ │ ├── rec.prmtop │ ├── 6K6E-01 │ │ ├── 6K6E-01.out │ │ ├── 6K6E.prmtop │ │ ├── 6K6E.rst7 │ │ ├── 6K6E_nowater.prmtop │ │ ├── 6K6E_nowater.rst7 │ │ ├── CATCH6K6En48.pdb │ │ ├── FINAL_RESULTS_MMPBSA.dat │ │ ├── equil40.mdcrd │ │ ├── equil40.pdb │ │ ├── lig.prmtop │ │ ├── mmgbsa.in │ │ ├── mmgbsa_run.out │ │ ├── mmgbsa_script.in │ │ ├── rec.prmtop │ ├── 6K6E-02 │ │ ├── 6K6E-02.out │ │ ├── 6K6E.prmtop │ │ ├── 6K6E.rst7 │ │ ├── 6K6E_nowater.prmtop │ │ ├── 6K6E_nowater.rst7 │ │ ├── CATCH6K6En48.pdb │ │ ├── FINAL_RESULTS_MMPBSA.dat │ │ ├── equil40.mdcrd │ │ ├── equil40.pdb │ │ ├── lig.prmtop │ │ ├── mmgbsa.in │ │ ├── mmgbsa_run.out │ │ ├── mmgbsa_script.in │ │ ├── rec.prmtop │ ├── 6K6E-03 │ │ ├── 6K6E-03.out │ │ ├── 6K6E.prmtop │ │ ├── 6K6E.rst7 │ │ ├── 6K6E_nowater.prmtop │ │ ├── 6K6E_nowater.rst7 │ │ ├── CATCH6K6En48.pdb │ │ ├── FINAL_RESULTS_MMPBSA.dat │ │ ├── equil40.mdcrd │ │ ├── equil40.pdb │ │ ├── lig.prmtop │ │ ├── mmgbsa.in │ │ ├── mmgbsa_run.out │ │ ├── mmgbsa_script.in │ │ ├── rec.prmtop │ ├── contacts │ │ ├── 6K6Econtacts.in │ │ ├── contacts.in │ │ ├── native.6K6D-01 │ │ ├── native.6K6D-02 │ │ ├── native.6K6D-03 │ │ ├── native.6K6E-01 │ │ ├── native.6K6E-02 │ │ ├── native.6K6E-03 │ │ ├── nonnative.6K6D-01 │ │ ├── nonnative.6K6D-02 │ │ ├── nonnative.6K6D-03 │ │ ├── nonnative.6K6E-01 │ │ ├── nonnative.6K6E-02 │ │ └── nonnative.6K6E-03 │ ├── hb_analysis │ │ └── hb_avg_summary.out │ ├── hbond_calc.in │ ├── mmgbsa.in │ ├── mmgbsa_script.in │ ├── nohup.out │ ├── nohup2.out │ ├── results │ │ ├── 6K6D-01FINAL_RESULTS_MMPBSA.dat │ │ ├── 6K6D-01alie.out │ │ ├── 6K6D-01equil40.pdb │ │ ├── 6K6D-02FINAL_RESULTS_MMPBSA.dat │ │ ├── 6K6D-02alie.out │ │ ├── 6K6D-02equil40.pdb │ │ ├── 6K6D-03FINAL_RESULTS_MMPBSA.dat │ │ ├── 6K6D-03alie.out │ │ ├── 6K6D-03equil40.pdb │ │ ├── 6K6E-01FINAL_RESULTS_MMPBSA.dat │ │ ├── 6K6E-01alie.out │ │ ├── 6K6E-01equil40.pdb │ │ ├── 6K6E-02FINAL_RESULTS_MMPBSA.dat │ │ ├── 6K6E-02alie.out │ │ ├── 6K6E-02equil40.pdb │ │ ├── 6K6E-03FINAL_RESULTS_MMPBSA.dat │ │ ├── 6K6E-03alie.out │ │ ├── 6K6E-03equil40.pdb │ ├── salt_bridge_calc.in │ └── sb_analysis │ └── sb_avg_summary.out └── structures ├── CATCH4K4Dn48.pdb ├── CATCH4K4En48.pdb ├── CATCH6K6Dn48.pdb └── CATCH6K6En48.pdb ``` ### catch-remd-repo.tar.gz The **catch-remd-repo.tar.gz** tarball contains file pertaining to the Replica Exchange Molecular Dynamics (REMD) simulations for single CATCH peptides. The *remd-catchff14sb* contains the subdirectories *6D*, *6E*, and *6K*, which correspond to the CATCH(6D-), (6E-), and (6K+) peptide, respectively. Within each CATCH peptide subdirectory contains the necessary files to replicate the REMD simulations and the final results. For more information regarding REMD and the purpose of these files, please refer to the [AMBER manual](https://ambermd.org/doc12/Amber20.pdf). For each system, we analyzed the secondary structure content for each system using the [Define Secondary Structure of Proteins](https://swift.cmbi.umcn.nl/gv/dssp/) (DSSP) algorithm. Output files are labeled as "dssp.out" and "dssp.out.sum". ``` . └── remd-catchff14sb ├── 6D │ ├── 6D.pdb │ ├── 6D.prmtop │ ├── dssp.out.sum │ ├── remd.310K.mdcrd ├── 6E │ ├── 6E.pdb │ ├── 6E.prmtop │ ├── dssp.out.sum │ ├── remd.310K.mdcrd └── 6K ├── 6K.pdb ├── 6K.prmtop ├── dssp.out.sum └── remd.310K.mdcrd ``` ### catch-stacking-repo.tar.gz The **catch-stacking-repo.tar.gz** tarball contains results and files relating to MD two separated bilayer simulations. Within *catch-stacking-10A-annealing* are subdirectories that are labeled systematically based on the CATCH system and the simulation run number, for example "6K6D-01" refers to the CATCH(6K+/6D-) system and is the 1st in a triplicate of simulations. Each directory that is labeled by a CATCH system name contains generally the following: the topology file (.prmtop extension), the input coordinates (.rst7 extension), along with the final simulation coordinates (equil*.mdcrd and equil*.pdb). For more information regarding these files, please refer to the [AMBER manual](https://ambermd.org/doc12/Amber20.pdf). The subdirectory *stacking-contacts* contains results for calculating the number of contacts between the two bilayers for the two separated bilayer simulations. The subdirectory *structures* contains a copy of the starting structures for each simulation system. ``` . └── catch-stacking-10A-annealing ├── 6K6D-01 │ ├── 6K6D.prmtop │ ├── 6K6D.rst7 │ ├── 6K6D_nowater.prmtop │ ├── 6K6D_nowater.rst7 │ ├── CATCH6K6Dn48.inp │ ├── CATCH6K6Dn48.pdb │ ├── equil1.mdcrd │ ├── equil40.mdcrd │ ├── equil40.pdb ├── 6K6D-02 │ ├── 6K6D.prmtop │ ├── 6K6D.rst7 │ ├── 6K6D_nowater.prmtop │ ├── 6K6D_nowater.rst7 │ ├── CATCH4K4Dn48.pdb │ ├── CATCH4K4En48.pdb │ ├── CATCH6K6Dn48.inp │ ├── CATCH6K6Dn48.pdb │ ├── CATCH6K6En48.pdb │ ├── equil1.mdcrd │ ├── equil40.mdcrd │ ├── equil40.pdb ├── 6K6D-03 │ ├── 6K6D.prmtop │ ├── 6K6D.rst7 │ ├── 6K6D_nowater.prmtop │ ├── 6K6D_nowater.rst7 │ ├── CATCH6K6Dn48.inp │ ├── CATCH6K6Dn48.pdb │ ├── equil1.mdcrd │ ├── equil40.mdcrd │ ├── equil40.pdb ├── 6K6Dnohup.out ├── 6K6E-01 │ ├── 6K6E.prmtop │ ├── 6K6E.rst7 │ ├── 6K6E_nowater.prmtop │ ├── 6K6E_nowater.rst7 │ ├── CATCH6K6En48.inp │ ├── CATCH6K6En48.pdb │ ├── equil1.mdcrd │ ├── equil40.mdcrd │ ├── equil40.pdb ├── 6K6E-02 │ ├── 6K6E.prmtop │ ├── 6K6E.rst7 │ ├── 6K6E_nowater.prmtop │ ├── 6K6E_nowater.rst7 │ ├── CATCH6K6En48.inp │ ├── CATCH6K6En48.pdb │ ├── equil1.mdcrd │ ├── equil40.mdcrd │ ├── equil40.pdb ├── 6K6E-03 │ ├── 6K6E.prmtop │ ├── 6K6E.rst7 │ ├── 6K6E_nowater.prmtop │ ├── 6K6E_nowater.rst7 │ ├── CATCH6K6En48.inp │ ├── CATCH6K6En48.pdb │ ├── equil1.mdcrd │ ├── equil40.mdcrd │ ├── equil40.pdb ├── 6K6Enohup.out ── stacking-contacts ├── 6K6D-01contacts.out ├── 6K6D-01equil40.pdb ├── 6K6D-02contacts.out ├── 6K6D-02equil40.pdb ├── 6K6D-03contacts.out ├── 6K6D-03equil40.pdb ├── 6K6Dcontacts.in ├── 6K6Dcontacts.out ├── 6K6E-01contacts.out ├── 6K6E-01equil40.pdb ├── 6K6E-02contacts.out ├── 6K6E-02equil40.pdb ├── 6K6E-03contacts.out ├── 6K6E-03equil40.pdb ├── 6K6Econtacts.in ├── 6K6Econtacts.out ├── native.6K6D-01 ├── native.6K6D-02 ├── native.6K6D-03 ├── native.6K6E-01 ├── native.6K6E-02 ├── native.6K6E-03 ├── nonnative.6K6D-01 ├── nonnative.6K6D-02 ├── nonnative.6K6D-03 ├── nonnative.6K6E-01 ├── nonnative.6K6E-02 └── nonnative.6K6E-03 ``` ### CATCH.DMD.tar.gz The **CATCH.DMD.tar.gz** contains the final results relating to PRIME20/DMD simulations. Provided are the coordinate files (.pdb extension) and files indicating the hydrogen bonding partners (.bptnr extension). More information regarding the simulations are provided in the associated manuscript and on the Hall group's [GitHub](https://github.com/CarolHall-NCSU-CBE/Serial-DMD-PRIME20). ``` . └── CATCH.DMD ├── 6K6Dt018-01run0508.pdb ├── 6K6Dt018-01run0509.bptnr ├── 6K6Dt018-02n0509.bptnr ├── 6K6Dt018-02run0509.pdb ├── 6K6Dt018-03n0509.bptnr ├── 6K6Dt018-03run0509.pdb ├── 6K6Et018-01n0509.bptnr ├── 6K6Et018-01run0508.pdb ├── 6K6Et018-02n0509.bptnr ├── 6K6Et018-02run0509.pdb ├── 6K6Et018-03n0509.bptnr └── 6K6Et018-03run0509.pdb ``` ## Code/Software Availability [PRIME20/DMD code](https://github.com/CarolHall-NCSU-CBE/Serial-DMD-PRIME20)