VMD-L Mailing List

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Thu Jul 05 2018 - 13:28:00 CDT

Hi Aoife,

something must have gone wrong when saving that file. The issue is the
following, QwikMD stores the topology files that you upload inside the
"~/qwikmd/toppar" folder, adding "_qwikmd" to the name of the file.
Additional to this, it adds an entry to the table in the file
"toppartable.txt" in the same folder containing the name of the residue,
the residue name defined in the topology, the type of molecule and the
associated file. If this is causing problems, I would delete the entry from
the file with the definition of you glycan, restart VMD, and I would repeat
the process of adding the topology, making sure to reset QwikMD after
adding the topology.

I hope this helps

Best

João

On Thu, Jul 5, 2018 at 12:04 PM AOIFE MARTHA HARBISON <
aoife.harbison.2013_at_mumail.ie> wrote:

> Hello João,
>
>
> Thank you for your reply. I seem to be able to include my renamed
> carbohydrate residue once I reset VMD, so thank you for your help. However
> I'm getting another error in trying to use the "prepare" tool. The error I
> usually receive is :
>
>
> couldn't open "/home/aoifeh/qwikmd/toppar/top_all36_carb_qwikmd_5.rtf": no
> such file or directory
>
>
> I've checked and no such file exists, and I've checked to see if I can
> download it, but have no such luck. Is it possible to download this file,
> or is this a file generated by qwikmd, and there is perhaps some other
> problem with the system? I'll include my files with this email, to give you
> a better indication of the situation.
>
>
> Thank you, kind regards,
> Aoife
> ------------------------------
> *From:* João Ribeiro <jribeiro_at_ks.uiuc.edu>
> *Sent:* Tuesday 3 July 2018 18:36:14
> *To:* AOIFE MARTHA HARBISON
> *Cc:* vmd_at_ks.uiuc.edu
> *Subject:* Re: Problem with QwikMD and glycans
>
> Dear Aoife,
>
> thank you for contacting us. As I understood, you added the topology file
> in QwikMD, and then you changed the name of the residue for a 4 letter
> residue in the topology table, is that correct? Did you reset QwikMD after
> that? When you load the structure after loading the topology file and
> resetting QwikMD, does QwikMD mark the residue in red? Did you change the
> name of the residue in the Structure Manipulation/Check window?
>
> It would be great if you could send the pdb and the topology file that you
> used.
>
> Best
>
> João
>
> On Tue, Jul 3, 2018 at 11:26 AM AOIFE MARTHA HARBISON <
> aoife.harbison.2013_at_mumail.ie> wrote:
>
> Hello,
>
>
> I'm trying to prepare a enzyme with a disaccharide in the binding site for
> QM/MM with NAMD, using QwikMD. I keep getting an error with autopsf,
> because it doesn't recognize one of my glycan's residue names (GlcNAc
> residue). I have edited the CHARMM name earlier as prompted by VMD when I
> added the carbohydrate topology file, and thought this might be the cause
> of the error, but it doesn't seem to recognize any 4 letter residue name I
> supply for it. Would you have any suggestions in fixing this problem? I'm
> using the 1.9.4a12 version of VMD as suggested for QM/MM simulation here
> http://www.ks.uiuc.edu/Research/qmmm/. Please let me know if there's any
> other files you need to see in order to understand the system.
> Hybrid QM/MM NAMD - University Of Illinois
> <http://www.ks.uiuc.edu/Research/qmmm/>
> www.ks.uiuc.edu
> Hybrid QM/MM NAMD. NAMD QM/MM interface extends existing NAMD features to
> the quantum mechanical level, presenting features that are not yet
> available in any QM/MM implementation.
>
> Kind regards,
> Aoife
>
>
>
> --
> ……………………………………………………...
> João Vieira Ribeiro
> Theoretical and Computational Biophysics Group
> Beckman Institute, University of Illinois
> http://www.ks.uiuc.edu/~jribeiro/
> jribeiro_at_ks.uiuc.edu
> +1 (217) 3005851
> 

-- 
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
http://www.ks.uiuc.edu/~jribeiro/
jribeiro_at_ks.uiuc.edu
+1 (217) 3005851