VMD-L Mailing List

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Tue Apr 11 2017 - 07:50:39 CDT

Dear Sharav,

please try to include as much details as possible for us to track the
problem properly (which protein are you using, the str file, etc.)

Please correct me if I'm wrong. You loaded a protein X in QwikMD and then
added the str file containing the topology and parameters information in
the "Topology & Parameters Selection" window, opened by the "Add
Topo+Param" button, in the "Structure and Manipulation/Check" window. When
you pressed apply in this window, did you have any error or was this error
generated when you pressed this button?

I would suggest to change a little bit the process. First add the the str
file and assign the correct molecule type while adding the file (are you
sure that the new topology is a nucleic acid residue?). Then reset QwikMD
to make sure that the topology is loaded and then load the protein X and
prepare the system.

Best

João

On Tue, Apr 11, 2017 at 3:32 AM Sharav Desai <sharavdesai_at_gmail.com> wrote:

>
> ---------- Forwarded message ----------
> From: "Sharav Desai" <sharavdesai_at_gmail.com>
> Date: 11 Apr 2017 11:38
> Subject: vmd-1
> To: <vr.hande_at_ncl.res.in>
> Cc: "Sharav Desai" <sharavdesai_at_gmail.com>
>
> hi,
>
> I have generated the str. file for new molecule and I also have edited the
> parameter in structure check window but when i tryIng to rename the resname
> following error comes. please give any suggestions to solve this problem.
>
> Thanks in Advance
>
>
>
>
> *Unable to create macro for 'qwikmd_nucleic'Unable to create macro for
> 'qwikmd_nucleic' while executing"atomselect macro qwikmd_nucleic
> $QWIKMD::nucleicmcr" (procedure "QWIKMD::UpdateRes" line 207) invoked
> from within"QWIKMD::UpdateRes $tbl $row $col $text" (procedure
> "QWIKMD::CallUpdateRes" line 2) invoked from
> within"QWIKMD::CallUpdateRes .qwikmdResGui.f1.fcol1.tableframe.tb 0 1
> CATE" ("uplevel" body line 1) invoked from within"uplevel #0
> $data(-editendcommand) [list $win $row $col $text]" (procedure
> "doFinishEditing" line 27) invoked from within"doFinishEditing $win"
> (procedure "finisheditingSubCmd" line 7) invoked from
> within"${cmd}SubCmd $win [lrange $args 1 end]" (procedure
> "tablelist::tablelistWidgetCmd" line 8) invoked from
> within"$QWIKMD::selresTable finishediting" invoked from within"if
> {[winfo exists .qwikmdResGui.f1.fcol1.tableframe.tb.body.f.e]} {
> $QWIKMD::selresTable finishediting*
>
>
> *I also have attached the log file.*
> *Regards..........*
>
>
>
>
>
>
>
>
>
> *SHARAV DESAIAsst. ProfessorDepartment of Pharmaceutical Microbiology and
> Biotechnology Pioneer Pharmacy Degree CollegeVadodara-390019M.no-9428128137*
>
>
> --
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
jribeiro_at_ks.uiuc.edu
+1 (217) 3000380