prepareforleap: An automated tool for fast PDB‐to‐parameter generation

Abstract

Setting up molecular dynamics simulations from experimentally determined structures is often complicated by a variety of factors, particularly the inclusion of carbohydrates, since these have several anomer types which can be linked in a variety of ways. Here we present a stand‐alone tool implemented in the widely‐used software CPPTRAJ that can be used to automate building structures and generating a “ready to run” parameter and coordinate file pair. This tool automatically identifies carbohydrate anomer type, configuration, linkage, and functional groups, and performs topology modifications (e.g., renaming residue/atom names) required to build the final system using state of the art GLYCAM force field parameters. It will also generate the necessary commands for bonding carbohydrates and creating any disulfide bonds.

MPI‐parallelization of the grid inhomogeneous solvation theory calculation

“…MD simulations were run on the FabI enoyl reductase protein from F. tularensis (PDB 3NRC). The PDB was preprocessed using the CPPTRAJ command “prepareforleap” 11 ; all solvent molecules and the triclosan residue were removed. The system was then aligned along principal axes using the CPPTRAJ principal command.…”

Function-structure approach reveals novel insights on the interplay of Immunoglobulin G 1 proteoforms and Fc gamma receptor IIa allotypes

“…All the simulations were performed in Amber 20 ( 51 ). The initial structure was generated by the prepareforleap module of Amber and then tleap was used ( 52 ). Minimization was done on the starting solvated structure with 1000 steps of steepest descent and 4000 steps of conjugate gradient with positional restraint on the protein with a force constant of 10.0 kcal/(mol.Å 2 ).…”