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
