On 12/4/13 11:03 AM, Mahboobeh Eslami wrote:
dear Justin thanks for reply I don't find tutorial for ATB and I don't know that which files are used for itp
It works much like PRODRG. You can upload coordinates or draw the molecule.
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?
It seems that if you want to upload your own molecule, the force field is 53A6. It is trivial to interconvert between Gromos parameter sets, though, by simple modifications. Of course, you can always derive the parameters from scratch yourself ;)
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 "GROMOS87" refers to the (outdated!)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 <mailto:jalem...@outerbanks.umaryland.edu> | (410) 706-7441 ==================================================
-- ================================================== 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.