Molecular Dynamics Simulation of a Designed Cyclic Peptide Bound to CTLA4

This data set for the manuscript entitled "Computational Design of a Cyclic Peptide that Inhibits the CTLA4 Immune Checkpoint Pathway" includes all files needed to run and analyze the simulations of a designed cyclic peptide (Peptide 16) bound to CTLA4 in the putative most stable binding configuration, which is detailed in Figure 6 of the paper. These files include molecular model structure files (NAMD psf), force field parameter files (in CHARMM format), initial atomic coordinates (pdb format), NAMD configuration files, NAMD output including restart files (in binary NAMD format) and trajectories in dcd format (downsampled to 10 ns per frame). Analysis is controlled by shell scripts (Bash-compatible) that call VMD Tcl scripts. These scripts and their output are also included. Version: 1.0 Conventions Used in These Files =============================== Structure Files --- - ctla4_P16_wat.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.) - ctla4_P16.pdb (initial coordinates before equilibration) - repart_*.psf (same as the above psf files, but the masses of non-water hydrogen atoms have been repartitioned by VMD script repartitionMass.tcl) - rest*.pdb (same as the above pdb files, but atoms have been marked for restraints in NAMD. These files are generated by doPrep.sh, with restraints applied to different atoms.) Force Field Parameters --- CHARMM format parameter files: - par_all36m_prot.prm (CHARMM36m FF for proteins) - toppar_water_ions_prot.str (CHARMM water and ions with NBFIX parameters needed for protein 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_rest.namd (NPT equilibration with different parts of the protein restrained) - template_prod.namd (for the long production ...