From: Kabir Biswas (
Date: Mon Apr 05 2021 - 17:45:40 CDT

We have been using QwikMD for generating input files for simulating protein structures. Now we would like to simulate small peptides requiring capping of the N- and C-terminal with ACE and NMA, respectively. We have been able to include these modifications to the peptide structure using Pymol, QwikMD does not recognize these and produces an error. We have also tried to provide specific parameter files for these modifications yet QwikMD produces the error. Has anyone tried using QwikMD for simulating capped peptides? If so, could you please provide a step-by-step protocol for the same?