I forgot to mention that are Ryckaert-Bellemans form dihedral for OPLS Force Field
Andres Ortega From: og_andre...@hotmail.com To: gmx-us...@gromacs.org Subject: RE: [gmx-users] dihedral doubt Date: Sat, 1 Mar 2014 23:54:06 +0000 Thanks Justin for your help, i will modify the i j k l of the dihedral in my topology to correspond to the bonded.itp Thanks again Andres Ortega > Date: Sat, 1 Mar 2014 18:39:04 -0500 > From: jalem...@vt.edu > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] dihedral doubt > > > > On 3/1/14, 6:27 PM, Andres Ortega Guerrero wrote: > > Thanks Justin for the advice and help, > > > > So i have to add in the bonded.itp > > O_2 C_2 CT OH with the parameters? or in the topology file (molecule) , y > > define the dihedral like OH CT C_2 O_2 ??? > > > > Either way. The dihedral's parameters either need to exist in any one of the > following: > > 1. In [dihedraltypes] in ffbonded.itp > 2. In the .top in a [dihedraltypes] directive declared before the first > [moleculetype] > 3. Explicitly printed on the line with the corresponding atom numbers in the > [dihedrals] directive > > If any of those is true, it will work. > > -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.