Dear Justin, >> Parameterization is a hard road that takes a lot of time
I agree and thanks for reply On Thu, Jul 25, 2013 at 3:47 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/25/13 8:41 AM, gromacs query wrote: > >> 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? >> >> > It is very hard to assign dihedrals based on approximations, and they are > generally not very transferable. Bonds and angles are easier, but > dihedrals are quite complex and the types and charges on atoms i and l have > a significant impact on the parameters. Shortcuts here will probably lead > to a bad topology. Parameterization is a hard road that takes a lot of > time, even for bonded terms that you think may be simple. > > -Justin > > 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 <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> >>> <htt**p://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<h**ttp://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> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> > -- > ==============================**==================== > > 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
