From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Fri Apr 24 2009 - 14:09:59 CDT

I finally solved the problem by forcing CHARMM to write a temporary
nonextended PSF file (with truncated atom types) which I used to solvate
the protein with psfgen. Then, I used again CHARMM to merge the solvation
box and the original extended PSF. NAMD seems to be able to deal with
extended PSF files so there shouldn't be problems during production. It's
not very elegant but it works.

Gianluca

On Fri, 24 Apr 2009, Gianluca Interlandi wrote:

> The main problem is that CHARMM is now using extened atom types with up to 8
> characters, e.g.:
>
> 7295 MANN 1 AMAN C1 CC3162 0.340000
>
> If I force CHARMM to write normal PSF without EXT than the atom type is
> truncated and this might cause other problems. I need to post a message to
> the NAMD mailing list and ask whether NAMD can handle extended atom types.
> Otherwise, I will have to manually rename the atom types in the topology and
> parameter files.
>
> 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.
>>
>>
>
> -----------------------------------------------------
> 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.
> -----------------------------------------------------
>
>

-----------------------------------------------------
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.
-----------------------------------------------------