VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Tue Apr 26 2011 - 11:43:56 CDT

psfgen doesn't support EXT format psf files yet, so it's probably choking
because it expects four bonds per line with a field width of 8.

-Jim

On Tue, 26 Apr 2011, John Stone wrote:

> Hi,
> It seems that psfgen doesn't like the X-PLOR format PSF file you've got,
> although the VMD PSF plugin seems to read it without trouble.
>
> Can you send me a gzipped copy of the PSF file that is causing you trouble?
>
> This is most likely a limitation of the PSF reader currently in psfgen,
> and is something we are looking at improving.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Apr 22, 2011 at 11:03:30AM -0400, Edward Lyman wrote:
>> Hi all,
>>
>> I am trying to use psfgen to delete a couple of lipids and write a new
>> psf/pdb pair. The toplogy files read in fine, but when I read teh psf, I
>> get:
>>
>> reading structure from psf file 50_50_10nm.xplor.psf
>> Error processing bonds
>>
>> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>> psfplugin) Detected a Charmm31 PSF file
>> psfplugin) Detected a Charmm31 PSF EXTEnded file
>> Info) Using plugin psf for structure file 50_50_10nm.xplor.psf
>> psfplugin) no cross-terms defined in PSF file.
>> Info) Analyzing structure ...
>>
>> I am running vmd 1.9, psfgen 1.5. The psf file is an xplor psf (runs in
>> namd) that was written by the charmm gui. The psf/pdb pair work just fine
>> for reading into vmd.
>>
>> Any help is appreciated.
>> Ed
>
> --
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> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
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>