VMD-L Mailing List

From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Fri Aug 10 2012 - 10:19:15 CDT

Thanks John.

I'll tell what I did.

1. I typed this in vmd tkconsole.
graphene -lx 2 -ly 2 -type armchair -nlayers 1 -b 1 -a 1 -d 1 -i 1
animate write psf graphene.psf
animate write pdb graphene.pdb

2. Then I created peptide YSSY using Peptide Builder

3.Then I used Merge Structure plugin and loaded psf and pdbs of above two
components. When I tried to merge this error message was displayed. Well I
don't understand much of this message.

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)

and in my terminal window there is a message "PSF is in charmm format
X-PLOR format is required"

Thanks
Monika

On Fri, Aug 10, 2012 at 2:29 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> I believe your error is due to an incorrect sequence of steps...
> The PSF files that VMD (and psfgen) write are always in the X-PLOR/NAMD
> variation of the CHARMM PSF format. The key difference between a PSF file
> that's formatted for X-PLOR/NAMD vs. one written by CHARMM, is that the
> X-PLOR/NAMD files store the atom types as text, whereas CHARMM stores them
> as numeric indices that correspond to the entries in the parameter
> file that will be used for the simulation. The X-PLOR/NAMD approach is
> more
> flexible since the atom types can be match by string comparisons, and the
> order of the particular parameter file doesn't matter.
>
> It is unclear what caused psfgen to emit the molecule destroyed error, but
> since you did not include the full sequence of commands you ran, I can't
> guess what you might have done wrong. Clearly however, psfgen is upset
> about something, most likely there's an incorrect sequence of operations,
> or you may have missed a step that psfgen requires. If you provide more
> detail, it should be possible for someone to help you out.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Fri, Aug 10, 2012 at 06:04:08AM +0000, Monika Madhavi wrote:
> > Dear all,
> >
> > I created a graphene sheet with Nanotube Builder and created psf and
> pdb
> > by typing
> >
> > "animate write psf graphene.psf"
> > "animate write pdb graphene.pdb"
> >
> > psf and pdb files were successfully created and then I wanted to
> merge it
> > with a peptide which I created using Peptide Builder using
> Mergestructure
> > plugin.
> > Then I got an error message saying
> >
> > "MOLECULE DESTROYED BY FATAL ERROR" and the exciting psf is in charmm
> > format but it need x-plor format.
> >
> > Then I tried to write psf using the command
> >
> > "animate write psf x-plor graphene.psf" as given in the psfgen user
> > guide,But then I got a psf file named x-plor.
> >
> > How can I convert my charmm psf to x-plor in vmd.
> >
> > Thanks
> >
> > Monika
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
>