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 -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
