VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 18 2017 - 10:18:06 CDT

Hi,
  I'm pretty sure that plugin was not developed/tested for special structures
like those produced by the carbon nanotube builder plugin that may need
special, or additional topology or parameter files. It was intended to
be used for straightforward PDB structures. You will probably be better
off to use psfgen or topotools yourself to combine the carbon nanotube with
your protein(s).

I'll see about looking at what the code is doing there and
making changes to the documentation to indicate this if the issues
I'm expecting are what is causing this error.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Sep 17, 2017 at 02:35:44PM +0530, Aishwarya Smriti wrote:
> Hi!
>
> I created a CNT using Nanotube builder plug-in of VMD (version 1.9.3) of
> dimension (5,10). I created pdb and pdf files by typingÂ
> set x [atomselect 0 "all"]
> $x writepdb cnt.pdb
> $x writepsf cnt.psf
>
> The psf and pdb files were successfully created. I wanted to merge this
> with a protein file, so I used Merge Structures plug in to which I got an
> error message as shown below:
>
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> Â Â Â while executing
> "readpsf $m2psf"
> Â Â Â invoked from within
> "psfcontext eval $psfcon {
> Â Â Â # this is a hack, just to get the topology file
> Â Â Â package require readcharmmtop
> Â Â Â set topologyfile [format "%s/top_a..."
> Â Â Â (procedure "mergeMolecules" line 6)
> Â Â Â invoked from within
> "mergeMolecules [list "$guiState(mergef1src).psf"Â
> "$guiState(mergef1src).pdb" ]Â [list "$guiState(mergef2src).psf"Â
> "$guiState(mergef2src).pdb" ]Â $gu..."
> Â Â Â (procedure "::MergeStructs::guiMergeConflictsResolved" line 6)
> Â Â Â invoked from within
> "::MergeStructs::guiMergeConflictsResolved"
> Â Â Â ("after" script)
> Please help me resolve this.
> Regards,
> Aishwarya
> Senior Undergraduate
> Chemical Engineering
> Indian Institute of Technology, Delhi 

-- 
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/