You might have better luck running pdb2pqr directly, instead of having pymol run it for you. I'd try downloading the recent version (I think it's on sourceforge), and possibly trying different forcefield parameters. You can then load the pqr file into pymol using apbs tools, or use it directly with apbs.
Pete
-----Original Message-----
From: CCP4 bulletin board on behalf of Philippe Leone
Sent: Fri 7/18/2008 3:46 AM
To: [log in to unmask]
Subject: [ccp4bb] electrostatic surface with Ca
Hi everybody,
I'd like to generate an electrostatic surface containing a Ca ion. I
tried to generate a pqr file to read it in Pymol, but the Ca is not
taken into account, so I tried to add directly the line correspondind to
the ion in the pqr file but it failed.
Any suggestion?
Philippe Leone
--
Philippe Leone, PhD
AFMB-CNRS
163 Avenue de Luminy Case 932
13288 Marseille Cedex 09
Tel: +33 (0)4 91 82 55 62
Fax: +33 (0)4 91 26 67 20
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