VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Aug 10 2012 - 09:29:08 CDT

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
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