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

[Jernej Zidar]

Dear all,
  In December 2011 I was asking about tips on how to port a Charmm
generalized forcefield for a polymer to Gromacs.

  I am happy to report that the forcefield was ported to Gromacs in a
way that allows the use of pdb2mx in order to create an initial
topology and .gro file.

  Major lessons learnt:
1. Read GROMACS manual, page 115 and on (repeat many times).

2. In the current working directory create a residuetypes.dat file
containing the list of all residues (monomers). Use the "Polymer" as
the descriptor, "Protein" will not work.

  The reason appers to be GROMACS interpreting the residues as
aminoacids despite they are not. In turn it expects said residues to
end with an oxygen atom (atomtype O; same as in aminoacids) the same
way aminoacids residues do.
  By changing the descriptor to "Polymer" I was able get rid of this error.

3. In the current working directory create a directory named cgen.ff,
use the /usr/share/gromacs/top/charm27.ff/ as the template to create
the necessary files.

  I will post the force field parameters along with some other force
field-related goodies on Gromacs site as soon as the paper will be
published.

  Thanks to all that helped.

Best,
Jernej