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 rep
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
f
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
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
