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

[Mark Abraham]

On 13/12/2011 5:06 PM, Jernej Zidar wrote:
> 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?
It can't. You must add to an existing .rtp file.

Mark