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\ -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Dyda > Sent: Sunday, June 12, 2005 5:38 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Pymol/ABPS > > > Hi, > > 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. > > It seems that APBS hates chain IDs. Is that really so, or > just my imagination? > > Thanks for your help. > > Fred > [32m********************************************************* > ********************** > Fred Dyda, Ph.D. Phone:301-402-4496 > Laboratory of Molecular Biology Fax: 301-496-0201 > HHS/NIH/NIDDK numerical page: 1-888-513-5421 > Bldg. 5. Room 303 e-mail: d...@helix.nih.gov > Bethesda, MD 20892-0560 URGENT message: > 8885135...@archwireless.net > ************************************************************** > *****************[m > > > ------------------------------------------------------- > This SF.Net email is sponsored by: NEC IT Guy Games. How far > can you shotput a projector? How fast can you ride your desk > chair down the office luge track? > If you want to score the big prize, get to know the little guy. > Play to win an NEC 61" plasma display: > http://www.necitguy.com/?r=20 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
