VMD-L Mailing List

From: Edward Lyman (edward.lyman_at_gmail.com)
Date: Fri Apr 29 2011 - 08:00:52 CDT

Thanks for the work around, it's very much appreciated. But, it occurs to me
now...why can't I simply use $sel writepsf blah.psf and $sel writepdb
blah.pdb from the vmd console to write out a psf and a pdb for selections
which delete the unwanted molecules? ie, why bother with psfgen at all when
you already have in hand a psf that contains all the correct force field
terms, etc, and you just want to delete a few molecules?

Thx,
Ed

On Tue, Apr 26, 2011 at 3:21 PM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:

>
> 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
>>>
>>>
>>