[gmx-users] Force field for polymer molecule - tips

[Jernej Zidar]

Hi.
 I would like to use a CHARMM (CGennFF based) of polymer molecule in
Gromacs. The polymer is composed of three different monomer and two
different terminal residues (one for each of the the two terminals) -
five residues in total.

 The CHARMM generalized FF has already been ported to Gromacs so
judging from the documentation
(http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field)
I should create a monomeres.rtp (arbitrary name?) file containing the
information about the monomeres. Any tips on doing that?

 The general workflow will be:
Generate the initial structure of the polymer of a given composition
using Charmm* and save the coordinates as a PDB (plus two other
files). Then supply the generated PDB to pdb2gmx to generate the
initial GRO file.

 Second question:
How will pdb2gmx "know" it has to parse the monomeres.rtp file?

* - so far the only package that can generate the initial structures
from a set of internal coordinates in the force field.

Thanks in advance,
Jernej Zidar