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 car
Dyda,
By default, PyMOL uses charges and radii from the Amber99 forcefield, as per
APBS. The PDB2PQR tool included with APBS enables you to use other
charge/radius sets, such as CHARMM.
Chain IDs need to be removed for PQR...though future versions of PyMOL do
this automatically.
Cheers,
Warren\
