Whoops! I accidentally replied only to James, rather than to the whole list.
PyMOL has some trouble with assigning charges. PDB2PQR handles it, but
manages to generate a bad PQR (missing the space between some columns with
leading minus signs, e.g. -100.2345-100.2345). Fixing the PQR file by hand
fixes the problem.
-michael
On Wed, Aug 5, 2009 at 11:35 AM, Warren DeLano <war...@delsci.com> wrote:
> 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 <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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--
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
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