On Sep 7, 2004, at 3:07 PM, Michael George Lerner wrote:
Fine so far. The Visualization tab is for visualizing an electrostatic
potential, so it won't make sense until after you've loaded a molecule
(your pdb file) and a map (most likely the electrostatic potential map
that APBS generates).
Oh, okay, that makes sense. And I forgot to mention before that I
currently have a total of 1GB of physical RAM, but I havent tinkered
with the size of swap at all, so it should be at factory default.
The pink dots flash around while PyMOL is assigning charges and
Hydrogens.
The WARNINGs later on aren't quite as harmless as you think ... do you
have any ligands or non-standard
residues?
Ah yes, there are substrates bound; maybe I should remove them first
from the pdb file?
Also, it looks like APBS never ran (or, if it did, it looks like APBS
failed to do anything useful). What happens if you open up a command
prompt in whatever directory you're working in and type
"/usr/local/bin/apbs pymol-generated.in" ?
I get the following info, with a couple errors at the end:
----------------------------------------------------------------------
APBS -- Adaptive Poisson-Boltzmann Solver
Version 0.3.1
Nathan A. Baker (ba...@biochem.wustl.edu)
Dept. Biochemistry and Molecular Biophysics
Center for Computational Biology
Washington University in St. Louis
Additional contributing authors listed in the code documentation.
Copyright (c) 2002-2004. Washington University in St. Louis.
All Rights Reserved.
Portions Copyright (c) 1999-2002. The Regents of the University of
California.
Portions Copyright (c) 1995. Michael Holst.
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
02111-1307 USA
----------------------------------------------------------------------
This executable compiled on Sep 2 2004 at 16:32:37
Vio_ctor2: some error occurred.
Vio_ctor: Vio_ctor2() failed.
Parsing input file pymol-generated.in...
NOsh_parse: Got pointer to NULL socket!
Error while parsing input file.
