VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 22 2013 - 10:24:02 CDT

Hi,
  I would suggest that you try one of the newer versions of VMD
which has updates to several of the tools you used below. It may
or may not solve the problem, but if the problem persists, it would
be much easier to track down in the current version of the code.
You can get the test versions of VMD 1.9.2 by following the instructions
posted here:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

Let us know if using the new VMD test version has any impact on
the problem you have been having.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, May 20, 2013 at 05:38:18PM +0000, Anurag Sharma wrote:
> Dear all,
>
> I created a (10,10) carbon nanotube with Nanotube Builder and created psf
> and pdb by typing
>
> "animate write psf cnt.psf"
> "animate write pdb cnt.pdb"
>
> psf and pdb files were successfully created (no problem regarding
> bonds,angles etc.) and then I wanted to merge it with a oligomer chain.
> So I used merge structure plugin in VMD.
>
> Then I got an error message saying
>
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> while executing
> "readpsf $m1psf"
> invoked from within
> "psfcontext eval $psfcon {
> # this is a hack, just to get the topology file
> package require readcharmmtop
> set topologyfile [format "%s/top_a..."
> (procedure "mergeMolecules" line 6)
> invoked from within
> "mergeMolecules [list "$guiState(mergef1src).psf"
> "$guiState(mergef1src).pdb" ] [list "$guiState(mergef2src).psf"
> "$guiState(mergef2src).pdb" ] $gu..."
> (procedure "::MergeStructs::guiMergeConflictsResolved" line 6)
> invoked from within
> "::MergeStructs::guiMergeConflictsResolved"
> ("after" script)
>
>
>
> Interstingly I have also tried to merge (9,9) and (8,8) carbon nanotubes
> with same oligmer chains and I found no problem there. I follow same
> procedures to generate carbon nanotubes and merging them with chains in
> all cases.
>
> I am using VMD 1.9.1 and nanotube 1.2 version.
>
>
>
> Thanks
>
> Anurag 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/