On Wed, Aug 31, 2011 at 8:23 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Dr. Vitaly V. Chaban wrote: >>> >>> Hi, ALL >>> >>> I have a question about the charge defined in the topology file. >>> It seems to me that the charge for each atom apprears twice in >>> different sections of the topology files. >>> >>> ------------------------------------------------------------------------------ >>> One is >>> [ atomtypes ] >>> ;name mass charge ptype c6 c12 >>> >>> The other is >>> [ atoms ] >>> ; id at type res nr residu name at name cg nr charge >>> >>> ------------------------------------------------------------------------------ >>> And the charge number in [ atomtypes ] are always 0.0. >>> Which one is actually read by gromacs program ? >> >> >> That one which is mentioned the last >> > > That is true in the case where grompp finds multiply defined types for > bonded interactions and atom types; the charges in ffnonbonded.itp are never > used by any program. The reason for their existence is not clear, but > perhaps they were used by older versions or were intended for some > streamlined force field organization that never came to fruition. >
I believe, this column is intended for aminoacids for which there should be a consistent set of parameters including charges. This is what we have in AMBER. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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
