Simulation Files for "Sequence Dependence of Folding and Self-Assembly of Glycine-X Repeat Peptides on Graphite"

This is the simulation data set for the manuscript: "Sequence Dependence of Folding and Self-Assembly of Glycine-X Repeat Peptides on Graphite". The current manuscript version is available on the ChemRxiv at: https://doi.org/10.26434/chemrxiv.15002765/v1 VERSION 1.0 of this repository============================= SIMULATION DATA===============Figure2_brute-T0.zip: Files from the large-scale simulations of GPGG-TTT:TTT-GPGG. Table2-3_analyze-folding-assembly.zip: Files from the large-scale simulations used to determine the folding and assembly states at 1.3 µs displayed in Tables 2 and 3 of the main tex and Table S1 of the Supporting Information, as well as the images in Figures S1, S2, S3, and S4 of the Supporting Information. Figure3_folding-T0.zip: Files from the calculation of folding free energy for GPGG-TTT:TTT-GPGG. Figure4_folding-turn.zip: Files from the calculation of folding free energy for different turn sequences. Figure5_folding-length.zip: Files from the calculation of folding free energy for different strand lengths. Figure6_folding-amino.zip: Files from the calculation of folding free energy for different strand GX repeats. Figure7_folding-coop.zip: Files from the calculation of folding free energy for folding of a peptide near two folded and paired identical peptides. Figure8-9_pairing.zip: The Pairing/ subdirectory contains files from the calculation of the free energy of pairing for different peptide sequences (TTT:TTT, GGG:GGG, AAA:AAA, EEE:ZZZ, EZE:ZEZ) and alignments (down2, down, mid, up, up2, up3). The Pairing/2_free_energy subdirectory contains the files for combining all the free energy calculations into a standard absolute binding free energy. The Spin/ subdirectory contains the files for calculating the PMF for rotation for isolated peptides. The files for calculation of the PMF along RMSD for isolated peptides are in another archive of this repository (Figure6_folding-amino.zip). The needed PMFs for the isolated RMSD and Spin are repeated in Pairing/2_free_energy/input for convenience. FEP.zip: Files from the calculation of the relative free energy of pair formation using alchemical free energy perturbation. FigureS6_terrace.zip: Files from the calculation of folding free energy in the presence of a graphite terrace. FigureS8_Amber.zip: Files from the calculation of folding free energy in the presence for different strand GX repeats with the Amber force field. CONVENTIONS USED IN THESE FILES =============================== Correspondence between file names and sequences (using the abbreviations defined in the paper):chp-T0: GPGG-TTT:TTT-GPGGchp-loop-GPGG-GGGG or chp-Tl1: GGGG-TTT:TTT-GPGGchp-TlD1: GDGG-TTT:TTT-GDGGhp-disu-zwit: GPGG-TTT:TTT-C–Cchp14aa: GPGG-T:T-GPGGchp-short-T0: GPGG-TT:TT-GPGGchp-long-T0: GPGG-TTTT:TTTT-GPGGchp-G0: GPGG-GGG:GGG-GPGGchp-A0: GPGG-AAA:AAA-GPGGchp-S0: GPGG-SSS:SSS-GPGGchp-D1: GPGG-DDD:DDD-GPGGchp-EX0 or chp-QEB: GPGG-EEE:ZZZ-GPGGchp-EX2: GPGG-EZE:ZEZ-GPGG Structure Files----------------- graph_*.psf (original NAMD (XPLOR?) format psf file including atom details (type, charge, mass), as well as definitions of bonds, angles, dihedrals, and impropers for each dipeptide.) - graph_*.pdb (initial coordinates before minimization and equilibration)- repart_*.psf (same as the above psf files, but the masses of non-water hydrogen atoms have been repartitioned by VMD script repartition.tcl)- freeTop_*.pdb (same as the above pdb files, but the carbons of the lower graphene layer have been placed at a single z value and marked for restraints in NAMD)- amber_*.prmtop (combined topology and parameter files for Amber force field simulations)- repart_amber_*.prmtop (same as the above prmtop files, but the masses of non-water hydrogen atoms have been repartitioned by ParmEd) Force Field Parameters----------------------CHARMM format parameter files:- par_all36m_prot.prm (CHARMM36m FF for proteins)- par_all36_cgenff_no_nbfix.prm (CGenFF v4.4 for graphene) The NBFIX parameters are commented out since they are only needed for aromatic halogens and we use only the CG2R61 type for graphene.- toppar_water_ions_prot_cgenff.str (CHARMM water and ions with NBFIX parameters needed for protein and CGenFF included and others commented out) Template NAMD Configuration Files---------------------------------These contain the most commonly used simulation parameters. They are called by the other NAMD configuration files (which are in the namd/ subdirectory):- template_min.namd (minimization)- template_eq.namd (NPT equilibration with lower graphene fixed)- template_abf.namd (for adaptive biasing force) Minimization-------------- namd/min_*.0.namd Equilibration-------------- namd/eq_*.0.namd Log Files---------For each NAMD configuration file, there is a log file with the same prefix, which gives the text output of NAMD. For instance, the output of namd/eabfZRest7_graph_chp1404.0.namd is eabfZRest7_graph_chp1404.0.log. Some log files have been omitted to reduce space usage. Large scale simulations------------------------ namd/coil0_*.0.namd (first run for replicate 0)- namd/coil0_*.1.namd (continuation from run 0 for replicate 0)- namd/coil0_*.2.namd (continuation from run 1 for replicate 0)...- namd/coil1_*.0.namd (first run for replicate 1)- namd/coil1_*.1.namd (continuation from run 0 for replicate 1)- namd/coil1_*.2.namd (continuation from run 1 for replicate 1) Replica-exchange umbrella sampling (free energy of folding)------------------------------------------------------------ namd/unfold_*.0.namd (simulation with altered Lennard-Jones parameters )unfold_nbfix2.prm) to unfold the peptide)- namd/refold_*.0.namd (simulation with normal parameters to refold it after unfolding)- namd/reus0_graph_*.0.namd (REUS, first run)- namd/reus0_graph_*.0.R0.log (Log file for replica R0 of the first REUS run)- namd/reus0_graph_*.0.R1.log (Log file for replica R1 of the first REUS run)...- namd/reus0_graph_*.1.namd (REUS, continuation)- namd/reus0_graph_*.1.R0.log (Log file for replica R0 of the REUS continuation) Adaptive biasing force calculations------------------------------------ namd/eabfZRest7_graph_chp1404.0.namd- namd/eabfZRest7_graph_chp1404.1.namd (continuation of eabfZRest7_graph_chp1404.0.namd) Simulation Output-----------------The simulation output files (which match the names of the NAMD configuration files) are in the output/ directory. Files with the extensions .coor, .vel, and .xsc are coordinates in NAMD binary format, velocities in NAMD binary format, and extended system information (including cell size) in text format. Files with the extension .dcd give the trajectory of the atomic coorinates over time (and also include system cell information). Due to storage limitations, large DCD files have been omitted or downsampled, creating new DCD files. These files are prefixed with stride100 or stride500, indicated only every 100 or 500 frames are kept, corresponding to an interval of 100 * 50000 steps/frame * 4 fs/step = 20 ns or 100 ns. The system cell trajectory is also included for the NPT runs are output/eq_*.xst. Scripts-------Files with the .sh extension can be found throughout. These usually provide the highest level control for submission of simulations and analysis. Look to these as a guide to what is happening. If there are scripts with step1_*.sh and step2_*.sh, they are intended to be run in order, with step1_*.sh first. Tcl scripts are usually VMD Tcl scripts and require VMD to run:vmd -dispdev text -e script.tcl -args [ARGUMENTS] There are also some standalone Tcl scripts, that can be run from tclsh. These will typically include #!/usr/bin/tclsh as the first line. There are also some Python scripts, meant to be run in Python 3. They often require the numpy and matplotlib packages.