From: Zachary E Tibbs (
Date: Mon Apr 08 2013 - 16:54:52 CDT

Hello all,

I would eventually like to run a NAMD/CHARMM simulation on my system. But, I am running into a problem when using VMD to prep the system--The problem occurs while trying to merge two pdb/psf pairs. One of these files is a protein for which I generated a psf for through psfgen, while the other is a small molecule which I submitted to the SwissParam server for psf generation/parameter calculations. I can open each pair in VMD using "mol new filename.psf; mol addfile filename.pdb" with no issues, leading me to believe that all files are in good order. I attempted to use the 'Merge Structures' extension to merge the two structures, as I have in the past. An update pops up stating, "No more segment name conflicts were detected...Merging structures," as normal. After clicking OK, I receive an error message "MOLECULE DESTROYED BY FATAL ERROR! ..." The details of the error lead me to believe that the error occurs while reading the small molecule psf--The error message is posted below.

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
    ("after" script)

I immediately attributed the problem to the fact that the small molecule psf was generated by the above named server--Something which I am new to use. But, after manual inspection of the psf files side by side, I came to the conclusion that the small molecule psf has a nearly identical setup as the protein psf--So I am at a loss for identifying the problem. It seems there is an issue with the small molecule psf file....But I assumed that a problem with the psf would disallow VMD to even read the file in the first place to open the structure. Has anyone experienced a similar issue who could offer guidance to resolve this problem? Any help would be tremendously appreciated. Thank you.