VMD-L Mailing List

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Fri Apr 24 2009 - 10:15:38 CDT

I created this PSF with CHARMM c35 by combining the new sugar paramter set
with the protein parameter set 22. I don't know whether it has anything to
do with that (extended atom types in the new sugar parameter set?) or with
version 35 of CHARMM. I dont't know how to tell CHARMM to create a psf
without EXT. I might either try to solvate the protein with CHARMM or to
create everything with psfgen from scratch. I will let you know which one
succeeds.

Gianluca

On Fri, 24 Apr 2009, Axel Kohlmeyer wrote:

> On Thu, 2009-04-23 at 23:41 -0700, Gianluca Interlandi wrote:
>> I am trying to solvate a protein using the solvate plugin of VMD. The PSF
>> (X-PLOR format) and PDB were produced with CHARMM. I get the following
>> error:
>>
>> vmd > solvate protein_xplor.psf protein.pdb -minmax {{-65 -65 -65} {65 65 65}}
>> reading structure from psf file protein_xplor.psf
>> Error processing bonds
>>
>> I'm using vmd version 1.8.6 on linux.
>>
>> I have uploaded the files here:
>>
>> http://artemide.bioeng.washington.edu/Files/protein_xplor.psf
>>
>> http://artemide.bioeng.washington.edu/Files/protein.pdb
>>
>>
>> Any help would be appreciated.
>
> try building a "normal" psf (w/o EXT). the readpsf command in psfgen
> seems to be not yet updated for handling newer style .psf files.
> work has been underway to interface psfgen to the molfile plugins,
> some of which in turn have been improved to read in more fields
> including angles and dihedrals. but as far as i can tell, it is not
> completed yet. i just tried compiling that variant of psfgen from
> the cvs and there are still some bugs. perhaps john knows more.
>
> cheers,
> axel.
>
>
>>
>> Gianluca
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>
>

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Gianluca Interlandi, PhD gianluca_at_u.washington.edu
                     +1 (206) 685 4435
                     +1 (206) 714 4303
                     http://artemide.bioeng.washington.edu/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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