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: CCP4BB@JISCMAIL.AC.UK 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 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
