VMD-L Mailing List

From: Aishwarya Smriti (smritiaishwarya85_at_gmail.com)
Date: Sat Sep 16 2017 - 05:19:34 CDT

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 typing

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. while
executing"readpsf $m2psf" 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)*

Please help me resolve this.

Regards,
Aishwarya
Senior Undergraduate
Chemical Engineering
Indian Institute of Technology, Delhi