From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Aug 10 2012 - 14:48:01 CDT

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.