From: Anurag Sharma (Anurag.Sharma_at_my.ndsu.edu)
Date: Wed May 15 2013 - 18:38:58 CDT

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