VMD-L Mailing List

From: Joao Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Wed Jan 29 2020 - 15:38:58 CST

Hi Soodabeh,

 

After you loaded the topology, did QwikMD recognized the residue defined in that topology? If not, you need to rename the unrecognized residue (in the Structure Manipulation/Check window) to match the residue name defined in the topology file. Also, make sure that the residue has the right molecule type (protein, nucleic residue, lipids, or hetero) defined. These steps are all described in the QwikMD (https://www.ks.uiuc.edu/Training/Tutorials/#qwikmd) tutorial and documentation page (https://www.ks.uiuc.edu/Research/vmd/plugins/qwikmd/)

 

The warning to reset QwikMD is to make sure that QwikMD loads the new topology file before loading the structure.

 

I hope this helps,

 

Best,

 

João

 

From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of soodabeh ghaffari <soodabehghaffari_at_gmail.com>
Date: Wednesday, January 29, 2020 at 3:24 PM
To: <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: question about an error in QuickMD

 

Hello,

I am a graduate student at Penn State. I am running an MD simulation with QwikMD. I have faced a problem and I would be most grateful if you could help me.

After loading the pdb file, I added topology file in the structure Manipulation, but when I pressed applied, I got a message saying "To ensure the proper load of the topologies, please reset QwikMD.

I started over the process, but the problem has still remained. I was wondering what resetting QwikMD means?

I am looking forward to hearing from you.

Best Regards,

Soodabeh