[gmx-users] Topology file for phosphothreonine (TPO) for OPLS force field
Bruce D. Ray
brucedray at yahoo.com
Sat Feb 6 18:17:09 CET 2010
On Sat, February 6, 2010 at 11:08:30 AM, Antoine Delmotte <antoinedelmotte at hotmail.com>
> Thank you very much for this, Bruce. It will help me, for sure.
> Could you just let me know where you found the parameters or how you
Most of the parameters came from the entry for threonine in ffoplsaa.rtp
The remainder came from running the most recent beta test version of
topolbuild 1.3 with the command line
/usr/local/bin/topolbuild -dir /usr/local/topolbuild -ff oplsaa -n tpo_pep -charge
which generates an OPLSaa topology with parameters found originally
in the Gromacs OPLSaa installation against a short peptide containing
phosphothreonine and sets the atom charges to the OPLSaa atom type
charges. I then edited the threonine entry from ffoplsaa.rtp according
to add in the phosphate atom types, and change those atom types that are
altered by the presence of the phosphate. Finally, I adjusted the charge
on the phosphorous from the charge given in ffoplsaanb.itp in order to
have the total charge come out as -2 for a fully ionized phosphate.
The exact ionization would depend on pH, of course, and I would have
to run the command for protonated TPO (TPH ? or TPH2 ? for the mono-
and di-protonated species?) to further correct atom types and charges.
Bruce D. Ray, Ph.D.
402 N. Blackford St.
Indianapolis, IN 46202-3273
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