VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun May 24 2015 - 03:58:34 CDT

On Sat, May 23, 2015 at 11:10 AM, Sanghamitra Debroy
<ee14resch12002_at_iith.ac.in> wrote:
> Dear Sir,
> I am trying to merge Nickel and graphene. Nickel is generated from dump xyz
> file using lammps and graphene is generated using vmd and then merging the
> two using pd and psf file.
> Initially i tried with VMD 1.9.1 and then with VMD 1.9.2 but getting the
> same error.

you are getting the error because the tool you are using is based on
psfgen which in turn requires your input to be compatible with the
select CHARMM forcefield topology and parameter files. this is
unlikely to exists for your nickel structure.

axel.

>
>
>
> ERROR
>
>
> 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)
>
> Thanks and regards
> Sanghamitra Debroy(Bhattacharjee)
> Research Scholar
> Phone No. 07569098994
> email id:- ee14resch12002_at_iith.ac.in
> IIT, Hyderabad
> A.P, India 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.