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
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
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
Thanks, Michael.
One further note- this problem can occur even with only a standard
protein (no alternate conformations, ligands, etc.). The solution is
simple: just replace all '-' characters with ' -'.
--James
On Aug 5, 2009, at 12:23 PM, Michael Lerner wrote:
Whoops! I accidentally
