VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Jul 17 2007 - 07:43:04 CDT

On Tue, 17 Jul 2007, naga raju wrote:

NR> Dear VMD users,
NR> I would like to calculate pka values
NR> of my protein using APBS plugins given in vmd. Would
NR> any one suggest tutorial for this plugins. How to
NR> convert PDB file to psf or pqr file in vmd with
NR> charge.

how about going over the APBS tutorial from nathan baker?

http://apbs.sourceforge.net/doc/tutorial/index.html

it _is_ being listed on the vmd APBSrun plugin page, BTW.

cheers,
    axel.
NR>
NR> Any suggestion is appreciated. Thank you in
NR> advance.
NR>
NR>
NR> with best regards,
NR> Nagaraju Mulpuri.
NR>
NR>
NR>
NR>
NR>
NR>
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-- 
=======================================================================
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.