VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Tue Apr 26 2011 - 14:21:01 CDT

If you can't get CHARMM-GUI to write a non-EXT, non-CHEQ format PSF (I
don't think you need either of those options) then try reading the file
into VMD, writing it out again, and using that file with psfgen.

If you use the psfgen binary from NAMD 2.8b1 you can probably read the
file with "readmol psf 50_50_10nm.xplor.psf" since that uses the VMD
plugins (I don't think VMD's psfgen module has plugins enabled yet).

-Jim

On Tue, 26 Apr 2011, Edward Lyman wrote:

> attached is the psf.
>
> Any suggestions for a workaround? I want to delete a couple lipid molecules
> as described in the psfgen docs...if there is some othe way to accomplish
> this, I am all ears.
>
> E
>
>
> On Tue, Apr 26, 2011 at 11:53 AM, John Stone <johns_at_ks.uiuc.edu> 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
>>
>> --
>> 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
>>
>