[AMBER] improper dihedral with gaff

From: Jio M <jiomm.yahoo.com>
Date: Thu, 18 Jul 2013 03:18:04 -0700 (PDT)

Dear All,

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? 

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.

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Received on Thu Jul 18 2013 - 03:30:02 PDT
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