VMD-L Mailing List

From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Fri Aug 10 2012 - 11:50:01 CDT

Thanks Axel. I'll try your suggestion but Its bit unclear to me what I have
to do with it. By the way, I am using vmd 1.9.1.

Thanks
Monika

On Fri, Aug 10, 2012 at 3:43 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Fri, Aug 10, 2012 at 4:29 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> > Hi,
> > I believe your error is due to an incorrect sequence of steps...
>
> ...and i believe the problem is due to an old version of the nanotube
> builder,
> i.e. a version of VMD prior to 1.9.1. here is the commit that fixes it.
>
> 2012-02-15 22:39 akohlmey
>
> * nanotube/: Makefile, graphene.tcl, gui.tcl, nanotube.tcl,
> pkgIndex.tcl:
>
> have the nanotube plugin assign segment ids to atoms so that
> psfgen no
> longer incorrectly identifies saved psf files as being in X-plor
> format.
>
> cheers,
> axel.
>
>
>
> > 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
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
>