VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Fri Apr 29 2011 - 08:12:56 CDT

That should work as well as anything, and if it doesn't we should fix it.

-Jim

On Fri, 29 Apr 2011, Edward Lyman 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?
>
> 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
>>>>
>>>>
>>>
>