- I apologize for resubmitting the question as my previous mail was not properly sent.
Dear gromacs users, I'm trying to build a new topology and a parameter file of a small organic molecule. My strategy is to use CGENFF(and <http://paramchem.org/> paramchem.org) to generate CHARMM topology and parameter, and then convert the topology with charmm2gromacs program. I have some questions on the process. 1) How is the 1-4 parameters generated from the CGENFF file(or more generally, from charmm ff?)? I was not able to find the parameters corresponding to the 1-4 nonbonded parameters in original CHARMM parameter files. I'd like to modify some parts of the topology and parameter obtained from <http://paramchem.org/> paramchem.org(adding new atomtypes, and change charges etc) before using charmm2gromacs and is curious if this may result in inconsistency of generated 1-4 parameters. Do I have to also change some other parameters, such as CMAP, when I'm modifying the charges, bond force constant, in the sake of correct 1-4 parameters? 2) As I understand from the CHARMM implementation paper of GROMACS, special features of CHARMM(multiple dihedrals, CMAP, etc) has been taken into the GROMACS package. I wonder at which step this is done. I guess maybe pdb2gmx does when it generates .top file, and this is taken into account when grompp processes .top file. I'm not sure if I'm correct. Thanks all in advance. I'm really appreciating the various features possible with GROMACS. Jong Wha -- 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
