gromacs

//TLDR Problem: On one of my recent projects, the ligand appeared intact during sorting stage but distorted after converting the stream file. Cause: This is caused by long ligand names, whihc distorts how the charmm2gmx script parses the stream file. Solution: Maintain ligand/residue name character count to 4 or below. Detailed explanation Parameterization of a ligand is a crucial step in molecular dynamics simulations.The detailed tutorial for this process is provided by Dr JA Lemkul on his website....