From: Sanghamitra Debroy (ee14resch12002_at_iith.ac.in)
Date: Sun May 24 2015 - 07:18:42 CDT

Then what can I do to solve this problem?
Looking forward for a reply.
On May 24, 2015 2:28 PM, "Axel Kohlmeyer" <akohlmey_at_gmail.com> wrote:

> 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.
>