VMD-L Mailing List

From: Herald Delis (bioinfo2021great_at_gmail.com)
Date: Sat Aug 07 2021 - 14:01:27 CDT

Dear VMD team,

I am trying to do QM/MM using the new version of VMD-QWIKMD (Version 1.9.4
LATEST ALPHA) on a metalloprotein.

*Problem:* The metal flies away in the preparation step.

*OS:* Tried on Windows10 and Centos7.5

*Background:*

My protein has 2 Fe ions at the active center and hydroxide and oxide ions
surrounding GLU and HIS residues.

I have edited the "toppar_water_ions_namd.str" file to include the Fe ion
and included this in the # C:\Program
Files\VMD\plugins\noarch\tcl\readcharmmtop1.2 # folder (and corresponding
in Linux). Although it identified the Fe and other ions, after adding the
str to "Add Topo + Params" and restarting VMD. Still, it flew away when I
press the prepare button.

*Question:*
1. Is there any way to restrain/constraint it?
2. Will it affect the QM/MM calculation? (Fe + surrounding atoms + GLU/HIS
residues are included in the QM region)

Thanks and regards,
H
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