Hi Jack, If you have AMBER you can define new residues pretty easily especially since you already have charges you like. Once you have a topology and coordinate file, "ambpdb -pqr -wrap -p FILE.top < FILE.crd > FILE.pqr" will generate a MEAD style pqr file.
Richard ------------------------------------------ Richard W. Dixon, Ph.D. Abbott Bioresearch Center 508-688-8008 richard.di...@abbott.com howa...@bromo.msbb.uc.edu (Jack Howarth) Sent by: pymol-users-ad...@lists.sourceforge.net 04/14/2005 06:44 PM To: pymol-users@lists.sourceforge.net cc: 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