VMD-L Mailing List
From: Anurag Sharma (Anurag.Sharma_at_my.ndsu.edu)
Date: Mon May 20 2013 - 12:38:18 CDT
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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
- Next message: Peterson J: "Suggestions on parameterizing a ligand to simulate in NAMD"
- Previous message: Filip Persson: "Obtain solvent-accessible surface vertices"
- In reply to: Anurag Sharma: "error in merging two structures"
- Next in thread: John Stone: "Re: error in merging two structures"
- Reply: John Stone: "Re: error in merging two structures"
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