From: Joao Ribeiro (
Date: Thu Mar 12 2020 - 15:33:17 CDT

Hi Jing,


Is there any more information before the error that you report?


The fact that QwikMD detected “your residue” means that the name of the residue that you loaded is defined in the topology files that the program loads by default. If your residue has the same name as one of the residues defined by the CHARMM force field, QwikMD will assume that everything is fine, but the preparation will fail.


If this is the case, please rename your residue and add the topology of the residue with the new name to QwikMD.


I hope this helps,






From: <> on behalf of jing liang <>
Date: Monday, March 9, 2020 at 10:39 AM
To: <>
Subject: vmd-l: Qwikmd for QMMM simulations




I am dealing with a small molecule for which I wrote a charmm topology file. Then,

I uploaded the small molecule pdb file and the topology file I created. After that,

I checked the structure and the option for topology was green. However, during

the preparation phase I got the following message:


Error during structure preparation: Autopsf error ERROR: failed on end of segment

MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over..


Do you know what is the issue? I have created the topology file for the small

molecule only but I haven't added the proper values in the parameter file because

I don't have them, for instance force constants, dihedrals, etc. I guess these

values will be ignored if I do a QMMM simulation where the small molecule is in

the QM region right?