AMBER Archive (2005)

Subject: Re: AMBER: Creating an input file for GRASP using AMBER 8

From: FyD (fyd_at_u-picardie.fr)
Date: Mon Feb 07 2005 - 13:52:42 CST

> I have a .pdb file of a protein which has approximately 1000 residues in
> it. I want to create an input file for GRASP which has the charge info in
> it, and was wondering if I can create such an input file using AMBER 8.

http://agave.wustl.edu/pdb2pqr/
to convert pdb files without charge into pdb files with charges

http://agave.wustl.edu/apbs/
to compute your electrostatic potential

http://www.scripps.edu/~sanner/html/msms_home.html
to compute your solvent excluded surface

http://www.scripps.edu/~sanner/python/pmv/index.html
to put all together.

All this is free & works under linux...

  F.-Y. Dupradeau
DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
The Scripps Research Institute, La Jolla, CA, USA
       --
http://www.u-picardie.fr/labo/lbpd/FyD.htm
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