On Fri, Sep 18, 2015 at 3:46 AM, Francesco Pietra <chiendarret.gmail.com>
wrote:
> Hello:
> I am trying to get the FF for a "small" molecule bearing a pseudoaromatic
> tricyclic system. Antechamber assigns atom type "cd" (= "cc") to a carbonyl
> carbon comprised, in a six-atom cycle, between to N atoms
>
>
> -N-CO-NH-
>
>
> In consequence, a number of unknowns arises:
>
> BOND K(kcal.mol-1.ang-2) Dist0(ang) Source
> cd-o
>
> ANGLE K(kcal.mol-1.rad-2) Theta0(deg) Source
> c -cd-na
> n -cd-o
> nc-cd-o
>
> DIHEDRAL Path V(kcal.mol-1.rad-1) Phase(deg.) Period Source
>
> IMPROPER V(kcal.mol-1.rad-1) Phase(deg.) Period Source
> ca-ca-ca-na
> cd-na-cc-nc
> c -cc-cd-na
> n -nc-cd-o
> c3-ca-na-cc
>
> Such data are not available in gaff.dat even on replacing "cd" with "cc".
> I could replace "cd" with "c", but in a perhaps too blind way of doing.
>
Did you use parmchk2 to find the parameters? This will look through the
database
and pick out parameters that best match what is in your molecule, and
assign a penalty score to show you how dissimilar your molecule is from the
original source of the parameters.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Sep 18 2015 - 05:00:04 PDT
