VMD-L Mailing List

From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Sun Aug 12 2012 - 19:51:20 CDT

Thank you very much Axel. That really worked!!!

Monika

On Fri, Aug 10, 2012 at 7:48 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Fri, Aug 10, 2012 at 6:50 PM, Monika Madhavi <monikamadhavi_at_gmail.com>
> wrote:
> > 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.
>
> you are right. i have too many different VMD versions installed
> on my desktop and confused the 1.9.1 release with a later
> alpha version. the bugfix that i mentioned was applied two
> weeks *after* the release of 1.9.1, so you cannot have it
> unless you install an alpha test version of VMD.
>
> you can easily fix your graphene psf file yourself by
> executing the following vmd script code on the VMD console.
>
> mol new graphene.psf waitfor all
> mol addfile graphene.pdb waitfor all
>
> set sel [atomslect top all]
> $sel set segid SHT
>
> animate write psf graphene-xplor.psf waitfor all
> animate write pdb graphene-xplor.pdb waitfor all
>
> and then use those new files that no longer confuse psfgen.
>
> axel.
>
> >
> > 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.
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
>