4493 Manuscript Data==================== author: Anton Hankesize of uncompressed folder: ~19Gb.DOI: 10.5281/zenodo.11470585 # Standard MD simulation data Standard Simulations were generated with gromacs 2021.5 using the charmm36m forcefield Juli 2021 release tarball (https://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36-jul2021.ff.tgz).Post processed (PBC) simulations are structured as follows:Mature generally refers to the wildtype 4493 antibody. - simulations/standardMD | |- prod.mdp example production mdp file used to run all production simulations. | |- mature Mature simulation set. (folder and file naming the same in all simulation directories) | |- {peptide}_{replicate}_prod.gro {peptide} = peptide; {replicate} = standard MD replicate | |- {peptide}_{replicate}_prod.tpr | `- {peptide}_{replicate}_prod_align_noPBC.xtc (10Frames/ns) | |- mature_rerun Additional set of replicates with the wildtype 4493. |- matureCapped Set of simulations with termini capped peptides |- mature_nanpv2 Set of simulations with NPDP similar positioning of NANP |- wo_pep Set of simulations without peptides for germline and mature `- germline Set of germline simulations. # RAMD simulation data RAMD simulations were generated with gromacs_2020.5 patched with RAMDv2 modified to account for the connected multiple ligand groups.(Source code provided as tar file ./sw/gromacs_ramd_patchv2.tar.gz) Not all trajectories contain an unbinding event (gromacs CUDA bug.). These trajectories were not considered in the analysis of simulations. - simulations/ramd | |- prod.mdp Exemplary production mdp file with RAMD settings, these were used in all trajectories w/ | differing RAMD random seed. | |- mature_2.625kcalmolA_4.0_3.0 | |- {peptide}_{replicate}_prod_{startFrame}.gro {peptide} = peptide; {replicate} = standard MD replicate; {startFrame} = Frame in standard MD used to start simulation. | |- {peptide}_{replicate}_prod_{startFrame}.tpr | |- {peptide}_{replicate}_prod_{startFrame}.ndx | |- {peptide}_{replicate}_prod_{startFrame}_align_noPBC.xtc (100Frames/ns) Files omited due to size -- available on request. | `- {peptide}_{replicate}_prod_{startFrame}_lastframe.pdb Last frame of the processed RAMD trajectory. `- gl_2.625kcalmolA_4.0_3.0 # Analysis - analysis | |- entropie Quasi harmonic entropy estimation. | |- inp Concatenated & Bootstrapped, coarse-grained and aligned trajectories of all systems | |- out CPPTRAJ runs to calculate QHE on the bootstrapped trajectories | |- run_complex.sh Script running analysis. | |- ana.py Script to calculte average and std of QHE for each system. (generates *.out *.tsv *.png) | |- cg.py Script used to bootstrap, coarse-grain align and build average structure with. | `- delta_entropies.ods Excel file used to calculate Tab 1. in Main text of paper from entropies.out. | |- mmpbsa MMPBSA calculations (MM + SolvEnergy) with gmx_MMPBSA | |- inp Input trajectories and topologies processed for MMPBSA | |- out/gmx_mmpbsa Output directories in which gmx_MMPBSA was run. | | ` *.dat Output files containing calculated energy terms from gmx_MMPBSA. | |- mmpbsa.in MMPBSA input file used to run analysis. | |- plot_results.py Python script to plot correlation of MMPBSA output with experimental data | |- pca_eig_extr.py Script to reduce simulations to regions of high probability density within trajectory (not used in the present analysis) | |- slurm-91315023.out Log file of the analysis run | `- run_mmpbsa.sh Shell script to run the MMPBSA analysis (generates input and output file trees). | `- ramd RAMD analysation. |- run.sh Shell script to run the analysis |- run_ramd_ana.py Python script called by `run.sh` to run the analysis using `ramdAnalysis.py` |- contact_clusters.py Python script to generate plots based on output of the analysis. |- ramdAnalysis.py Python module containing analysis classes called/used within `run_ramd_ana.py` | Based on tauRAMD & Fingerprint analysis by Dr. Daria Khokh (https://doi.org/10.1021%2Facs.jctc.8b00230; https://doi.org/10.1063%2F5.0019088) |- abrun.* Log files from the present run |- *.svg; *.png Analysis output files. |- tramd_patchv2/ Output PDB structures from the analysis (excluded due to size, available on request) `- representatives.pse Pymol session of cluster representatives along unbinding for germline and wildtype with contact probabilities within the cluster mapped as b-factor. # Figures - figure_pdbs PDB files (and pymol sessions) used to generate figures in the papers main text.