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-- Dr. Dean Cuebas, Associate Prof of Chemistry deancuebas.missouristate.edu, Ph 417-836-8567 FAX 417-836-5507 Dept. of Chemistry, Missouri State University Springfield, Missouri 65897 > From: Dmitry Nilov <nilovdm.gmail.com> > Reply-To: AMBER Mailing List <amber.ambermd.org> > Date: Thu, 15 Apr 2010 05:05:13 -0500 > To: AMBER Mailing List <amber.ambermd.org> > Subject: Re: [AMBER] How do you know when to include improper dihedrals???? > > Notice, that only nicotinamide part is described in frcmod by Ross Walker. > And it seems to me, that he developed proper dihedral parameters in > the manner allowing to keep nicotinamide ring planar. In general, parmchk > should give you reasonable impropers. > > On Mon, Apr 12, 2010 at 11:30 PM, Dean Cuebas > <deancuebas.missouristate.edu>wrote: > >> Dear amberers, >> >> I guess my question is more to Ross Walker, since he is the one whose >> parameterized NAD+ files I am referring to, but I'll accept a clarification >> from anyone! :-) >> >> Using the .mol2 file with charges and amber atomtypes for NAD+ with parmchk >> and the parm99.dat file, a frcmod file is created that contains improper >> dihedrals for the aromatic adenine ring system. Yet, in the frcmod file >> provided by Ross Walker, there are no such improper dihedrals specified. >> >> First let me say that I am not implying a mistake on Ross's part, because >> I've seen a few other instances where this is the case also. >> >> So my question is, when are the impropers that are supplied in the frcmod >> file produced by parmchk not necessary? >> >> For example, I have a compound I am parameterizing that contains planar >> amides and planar thioester linkages. Using parmchk with the parm99.dat >> file >> gives me impropers in the frcmod file with for each of these, with a large >> force constant of 10.5. >> >> Do I need these specifications for these planar linkages?? >> How do you decide??? >> >> Thanks so very much for your help in advance. >> >> With regards, >> >> Dean >> >> >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > > > > -- > Dmitry Nilov, > Lomonosov Moscow State University > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Apr 15 2010 - 08:30:04 PDT