VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Aug 10 2012 - 10:43:03 CDT

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.