I think acepype Amber2gromacs tool has amber parameter files. but here is no .rtp
On Thu, Mar 6, 2014 at 4:40 PM, Chetan Mahajan <chetanv...@gmail.com> wrote: > Thanks, Justin. I do not have AMBER parameter set or .rtp file. I have > just one .top file which contains topologies and parameters. Just curious: > where to get Amber parameter set from? > > > On Thu, Mar 6, 2014 at 4:25 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 3/6/14, 5:16 PM, Chetan Mahajan wrote: >> >>> Hi >>> >>> I just wanted to check the order of atoms in a improper in gromacs input >>> file *.top. According to urea example on page 137 ( section 5.7)of manual >>> 4.6.4, order of i,j,k,l atoms in improper always starts with central >>> atom, >>> whereas that in a *.top file generated with acepype lists i,j,k,l order >>> for >>> improper in formate ion as H O C O. Central atom at third position. Is >>> this >>> right or bug in the tool acepype? >>> >>> >> It's right. The example in the manual is for Gromos force fields. You >> should look at the actual .rtp files for the AMBER parameter set you're >> trying to use. Suffice it to say that different atom orders are supported, >> because the Gromacs machinery (specifically pdb2gmx) knows how to deal with >> lots of stuff based on bonded geometry. >> >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Ruth L. Kirschstein NRSA 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 >> http://mackerell.umaryland.edu/~jalemkul >> >> ================================================== >> -- >> 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. >> > > -- 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.