[gmx-users] defining new residues?

[scott.t.milner at exxonmobil.com]

Hello -- I am interested in using gromacs to simulate polymers.  Apparently
the .rtp files within gromacs are defined for protein residues, not typical
monomers being used in polymers.  I don't know anything about proteins, but
I would think that there is a strong analogy between proteins and polymers,
in that linear polymers are composed of a succession of monomers (often,
just the same monomer repeated), joined by single covalent bonds.  Typical
monomers I would be interested in are methylene (-CH2-), propylene
(-CH(CH3)CH2-), styrene (-CH(C6H5)CH2-), and so forth.  It would be very
convenient if I could add these structures as new "residues" to the
definitions of some of the force fields (e.g., OPLSAA and GMX), so that I
could use pdb2gmx to generate topology files for a simulation, without
having to generate the topology files by hand.  Is there some documentation
that describes the structure of the various files associated with a force
field, and what information would then be required for defining new
residues?

Thanks for any help you can provide --

Scott Milner
ExxonMobil Research and Engineering
1545 Route 22 East
Annandale, NJ  08801
(908) 730-2309 phone
(262) 313-2583 fax