On Sun, 12 Jun 2005, Dyda wrote:
I'd like to know what charges Pymol uses when
generates a pqr file from a pdb.
The follow-up would be is whether there was
a way to change this, say if one wanted to
use charmm charges rather than amber.
PyMOL uses amber99 charges and radii. This is taken care of in
pymol/modules/chempy/champ/amber99.py. It would be possible to add a
different forcefield by using that as a template and changing a few things
in pymol/modules/chempy/champ/assign.py, but it would take more free time
than I have right now.
It seems that APBS hates chain IDs. Is that
really so, or just my imagination?
This is true, but has been fixed in the current version of the PyMOL/APBS
Plugin. Warren has added a couple of other nice features to the current
version. Here's a copy of a message that I just sent to the APBS list:
Hi all,
This is fixed in the current PyMOL source tree, and it'll be fixed in the
next released version of PyMOL. In the meantime, you can
download the current version here:
http://www-personal.umich.edu/~mlerner/PyMOL/apbs_tools.py
There are installation instructions at the top of
http://www-personal.umich.edu/~mlerner/PyMOL/
but it boils down to "replace your
$PYMOL_PATH/modules/pmg_tk/startup/apbs_tools.py with the current one."
There are a few other new features, including:
- More reasonable starting dielectric constants
- The ability to set a maximum number of grid points
- The ability to display solvent accessible surfaces as well as molecular
surfaces
- Better warnings when PyMOL is unable to generate appropriate parameters
in the PQR file.
Sometime soon, I'll probably also change the .in file to say things like
"bcfl sdh" instead of "bcfl 1" etc.
Given that the PyMOL/APBS Plugin is getting updated a bit, please let me
know if there are any features/changes you'd like.
thanks,
-michael
--
www.umich.edu/~mlerner | _ |Michael Lerner
This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan
it's a cheer-ocracy. | - against HTML email X | Biophysics
-Torrence, Bring It On| / \ | mler...@umich
