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 W. Dixon, Ph.D.
Abbott Bioresearch Center

howarth@bromo.msbb.uc.edu (Jack Howarth)
Sent by: pymol-users-admin@lists.sourceforge.net

04/14/2005 06:44 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

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