VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Apr 29 2011 - 08:40:55 CDT

On Fri, Apr 29, 2011 at 9:00 AM, Edward Lyman <edward.lyman_at_gmail.com> wrote:
> 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?

you can do this. the functionality to store and write out the complete topology
information from and to .psf files has not been around that long and before that
using psfgen was the only option. not everybody is aware of this new
functionality
in VMD and various plugins and scripts are only slowly being migrated to make
use of these new features (why break something that works?).

cheers,
    axel.

>
> 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
>>>>
>>>
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.