Re: [AMBER] improper dihedral with gaff

From: David A. Case <case.biomaps.rutgers.edu>
Date: Thu, 18 Jul 2013 11:43:19 -0400

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?

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
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