Jack, Editing the output PQR sounds like a sensible approach.
As far as obtaining charges goes: in order to be quantitatively correct, the ligand would need to be parameterized using the same approach as the protein force field...(for Amber99, I think that means performing an ab initio quantum calculation and then fitting the resulting charges using RESP...). Using charges from another forcefield could be mixing apples and oranges...though its probably fine for a qualitative figure. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . 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 > Jack Howarth > Sent: Thursday, April 14, 2005 3:45 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] SEPs in pymol generated pqr > > What is the recommended approach with apbs for creating > a pqr file from a pdb which has SEP residues? Under gromacs I > have been able to do MD on this peptide by using the user > donated ffG43a1p force field which supports phosphoserine > residues. Unfortunately none of the force fields available at > the PDB2PQR web site supports the SEP residue type. Should I > just let pymol create a pqr from the pdb and manually edit > resulting pqr (which at least retains its SEP residues upon > conversion although no charges or radii are writen out)? > However I am still uncertain of what values to use for the > SEP residues. The ffG43a1p.rtp shows... > > [ SEP ] > [ atoms ] > N N -0.28000 0 > H H 0.28000 0 > CA CH1 0.00000 1 > CB CH2 0.00000 2 > OG OA -0.36000 2 > P P 0.94000 2 > O1P OP -0.86000 2 > O2P OP -0.86000 2 > O3P OP -0.86000 2 > C C 0.380 3 > O O -0.380 3 > > Of course this is with some of the protons deleted from the > -ignh flag in pdb2gmx. > > Thanks in advance for any advice on how to be handle this issue. > Jack Howarth > > > ------------------------------------------------------- > SF email is sponsored by - The IT Product Guide Read honest & > candid reviews on hundreds of IT Products from real users. > Discover which products truly live up to the hype. Start reading now. > http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
