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: pymol-users@lists.sourceforge.net
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

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