From: Mariano Spivak (mariano_at_ks.uiuc.edu)
Date: Fri Dec 24 2021 - 17:11:54 CST

Hi Ahmad,

Are you running the latest alpha for VMD?
If you are able to share (privately) some example files, and the steps to reproduce the error, I can take a look and see if there is bug in the code.

Best

> On Dec 24, 2021, at 3:25 PM, Ahmad Alqaisi <aalqais2_at_asu.edu> wrote:
>
> Hello,
>
> 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 process.
>
> 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 exactly.
>
> If you can give any hint to what might be the problem, that would be great
>
> Ahmad Alqaisi