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.