From: Ahmad Alqaisi (
Date: Fri Dec 24 2021 - 15:25:30 CST


I have used the QwikMD tool in VMD to generate NAMD input successfully tens
of times, mostly for protein-ligand systems, and I'm very familiar with the

But, in some cases, after adding the FF str file for the ligand and
clicking "prepare" to generate the input files, after the preparation the
ligand structure in the system is distorted in a very strange way

In all of the cases, I checked everything that could cause this problem,
like the directory name, ligand FF file. missing chains or any other
reason that may have caused the issue, and I haven't figured the problem

If you can give any hint to what might be the problem, that would be great

Ahmad Alqaisi