Dear Justin, Thanks this paper is quite explained and requires much detailed study (sorry am escaping!) As I have these two params missing, is there any tool that can help me in this regard or may be some approximation method I may use?
thanks On Thu, Jul 25, 2013 at 3:28 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/25/13 8:25 AM, gromacs query wrote: > >> Dear All, >> >> I am working on some molecule and I have defined atom types with OPLSaa >> and >> all atom types really exist in oplsaa and well chosen so no approximation >> in choosing atom types. During grompp, I found there are dihedral param >> missing. e.g. >> N CT CT NT >> N CT CT N3 >> >> Is there any 'good' way of finding/assuming dihedral params for this? or I >> should choose values of some nearby atom types? >> >> > The OPLS dihedral fitting strategy is exceptionally well explained in the > Kaminski 2001 paper (reference in Gromacs manual). > > -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 > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) > 706-7441 > > ==============================**==================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
