[AMBER] How to apply extra dihedrals

From: Lekpa Duukori <duukori.gmail.com>
Date: Tue, 16 Mar 2010 09:19:18 -0600

Hi Everyone,

I have a question about how extra dihedrals are applied.

My study involves a situation where I need to apply an extra N-CT-CT-AO
dihedral ( AO being a new atom type ).

I make a frcmod file as follows

N -CT-CT-AO 1 0.156 0.0 -3.
N -CT-CT-AO 1 2.839 0.0 2

with the first line being the original generic X-CT-CT-X included in the
AMBER .dat files.

My question is: does AMBER still apply this X-CT-CT-X term to my dihedral as
that would be double counting?

Another option would be to edit the parmset in xleap and add only the new V2
dihedral but I am not sure if it also applies the generic one in this case
as in the parmset X-CT-CT-X does not have the negation on PN.


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Received on Tue Mar 16 2010 - 08:30:02 PDT
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