VMD-L Mailing List

From: Joao Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Wed Jan 29 2020 - 16:11:01 CST

Oh, sorry if I was not clear.

 

Reset, means pressing the “Reset” button on the QwikMD’s main window.

 

Again, if there is no unparameterized/unrecognized residue, you don’t need to provide more topologies to QwikMD unless some other reason is escaping me right now.

 

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 4:06 PM
To: Joao Ribeiro <jribeiro_at_ks.uiuc.edu>
Cc: Vmd l <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: question about an error in QuickMD

 

Hi,

Why do you mean by reset QwikMD? You mean closing QwikMd and opening again?

 

On Wed, Jan 29, 2020 at 4:54 PM Joao Ribeiro <jribeiro_at_ks.uiuc.edu> wrote:

Hi Soodabeh,

 

Please keep vmd-l in the chain.

 

So why do you want to provide those topologies to QwikMD?

 

Once you added the topology files, pressed “Apply”, and reset QwikMD, were you able to see those topology files listed in the table? If they were listed, you don’t need to add again.

 

Best,

 

João

From: soodabeh ghaffari <soodabehghaffari_at_gmail.com>
Date: Wednesday, January 29, 2020 at 3:49 PM
To: Joao Ribeiro <jribeiro_at_ks.uiuc.edu>
Subject: Re: vmd-l: question about an error in QuickMD

 

Hi Joao,

Thank you for the response.

I am sure that the residue has the right molecule type ( it is lipid). Also, there is no unrecognized residue. Please see the screenshot attached.

I worked with QwikMD previously, but I did not have this problem.

I would appreciate your help.

On Wed, Jan 29, 2020 at 4:39 PM Joao Ribeiro <jribeiro_at_ks.uiuc.edu> wrote:

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