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
>
>
>
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>
--
Dmitry Nilov,
Lomonosov Moscow State University
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Received on Thu Apr 15 2010 - 03:30:02 PDT
