You could look at amber10/dat/leap/prep/all_amino94.inand amber10/dat/leap/prep/
all_nuc94.in to learn how to use impropers in amino acids and nucleic
acids. Also you could check p.261 of Amber 8(!) manual.
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 - 06:00:02 PDT
