VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue May 13 2008 - 17:31:47 CDT

On Tue, 13 May 2008, ffavela_at_fis.cinvestav.mx wrote:

FF> Hi everybody.

fernando,
 
FF> I have the pdb and itp files of a POPG membrane that was built and ran using
FF> gromacs and that I now want to run with NAMD. Is there anyone who can tell
FF> me how to convert the itp file into charmm topology format so I can run it
FF> with namd?

there is a number of things that you can try. e.g., have a look at:
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/

this script works best a preprocessed .top file (you have top build
a real GMX input and then run grompp).

and for a description of the file formats (in case you want to write
your own converter or do it manually) you might want to check out:
http://www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/forcefield-html/node6.html

cheers,
   axel.

p.s.: and if you get it to work well, don't forget to send in the
resulting files so they can be bundled with future versions of the
membrane builder... ;-)

FF>
FF> Regards
FF> Fernando.
FF>
FF>
FF>
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FF> 

-- 
=======================================================================
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.