VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun May 24 2015 - 07:36:55 CDT

On Sun, May 24, 2015 at 2:18 PM, Sanghamitra Debroy
<ee14resch12002_at_iith.ac.in> wrote:
> Then what can I do to solve this problem?

most importantly, think logically!

there is no general advice, since you don't say what you need to the
resulting output for. that very much determines what kind of
information has to be created and or preserved. potential solutions
are:
- augment some existing CHARMM topology/parameter files so that psfgen
doesn't fail
- write such file specifically for your structure from scratch (since
you have only two types of atoms in there, it should be doable)
- use a different way to merge structures (e.g. using LAMMPS itself or
the topotools plugin in VMD).
- use a text editor (requires detailed knowledge of the underlying
file formats).
- write a custom script to generate the merged geometry and topology.

axel.

> 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. 

-- 
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.