On Thu, Jul 18, 2013, Jio M wrote:
>
> My molecule is defined with GAFF and there is peptide bond in it. With
> parmchk it does not write any other required params required.
>
> 1) Do I need to define in frcmod the improper for peptide bond or it can
> pick itself from gaff.dat dihedrals?Â
The required parameters will be be read in from gaff.dat.
>
> 2) In gaff.dat there are just dihedrals; does it include both improper
> and proper dihedrals and as gaff potential says both (proper and
> improper dihedrals) are governed by same equation? If yes, then which
> atom is considered as central atom for improper dihedral.
Gaff.dat has both dihedrals and improper dihedrals. The central atom is
always number three in the list of four atoms.
...dac
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Received on Thu Jul 18 2013 - 09:00:02 PDT
