From: Warren D. <wa...@de...> - 2009-08-05 15:38:37
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James, It sounds like there mayy be something other than canonical amino acids in your structure which might need to be removed prior to performing a calculation. These may be alternate conformations of amino acid side chains, ligands, or other unrecognized groups which cannot be processed for APBS. Cheers, Warren -----Original Message----- From: James Whittle [mailto:whittle@MIT.EDU] Sent: Wed 8/5/2009 5:01 AM To: pym...@li... Subject: [PyMOL] problems with apbs/pqr Hi all, My apologies if this has been covered by this list before, but I couldn't find mention of it: I'm trying to calculate an electrostatic surface for my protein. The APBS Tools plug-in crashes with the message: WARNING: 502 atoms did not have formal charges assigned WARNING: 1051 atoms did not have properties assigned This happens whether I use a pqr file from PDB2PQR or the PyMol generated PQR. I'm running OS X (Intel), Pymol version 1.2r0. I also tried it though on a linux machine, and got the same error. This plug-in works fine with several other coordinate files. I tried removing the chain ids from the pdb file, but that did not help. Can anyone offer any advice on this? --James ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ PyMOL-users mailing list (PyM...@li...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... |