dear Justin thanks for reply I don't find tutorial for ATB and I don't know that which files are used for itp and gro files from ATB result, Moreover in gromacs site is mentioned that PRODRG is used for GROMOS96 force field, 43A1. can I use ATB for 43A1 force field?
On Wednesday, December 4, 2013 7:07 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 12/4/13 10:24 AM, Mahboobeh Eslami wrote: > hi dear Justin > > You've written the following context in your tutorial: > > > Force field (GROMOS96.1/GROMOS87): "GROMOS96.1" refers to the first version > of the GROMOS96 force field, 43A1. "GROMOS87" refers to the (outdated!) > GROMOS87 force field. Choose "GROMOS96.1" to get 43A1 parameters for our > ligand > > but I don't see the option for Select the force field in PRODRG server PRODRG is now hosted by a company, so I don't know what sorts of changes they have introduced. There is no more force field selection, so it's a black box, I suppose. Given that you probably have to re-write the topology anyway, it probably doesn't matter much except for a few atom types that may be different between the force fields. ATB is probably a better option; I think its output is generally much more reliable than PRODRG. I'll probably revise the tutorial at some point, but the use of PRODRG to get a flawed topology is a good teaching tool. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
