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:whit...@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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