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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
