VMD-L Mailing List

From: soodabeh ghaffari (soodabehghaffari_at_gmail.com)
Date: Wed Jan 29 2020 - 16:13:01 CST

Thank you very much for your help.

On Wed, Jan 29, 2020 at 5:11 PM Joao Ribeiro <jribeiro_at_ks.uiuc.edu> wrote:

> 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
>
>