[AMBER] Setting exclusions correctly

From: Arun Srikanth <askforarun.gmail.com>
Date: Mon, 13 Oct 2014 03:12:15 -0400

Hello amber users. I am using the GAFF force field in my simulations. I
have a couple of questions

1. Is the scaling factor for the AMBER force field same for GAFF (1/2 and
1/1.2 for vdw and eel respectively )for all 1-4 interactions (whether they
define a dihedral or not)

2. The second question is regarding my earlier post. I had raised a
question on what the "M" indicates when one uses parmed.py to print
dihedrals. The reply from Dr. Jason was

A "M" indicates that
"the end-group interactions are neglected (i.e., the 1-4 vdW and 1-4
electrostatic interactions are not calculated for that torsion). This
occurs in rings with 6 atoms or fewer and for all but one term of a
multi-term dihedral (I originally chose "M" to indicate "multiterm", but
it also applies to ring torsions that have only 1 term but whose
end-groups are excluded by virtue of being 1-3 or 1-4 partners of a
different group)."

I have benzene ring in my system

As such the GAFF force includes the vdw and eel (scaled) for all 1-4

Should one specfically exclude the the eel and vdw when M is printed for
those dihedrals ?

Can someone please clarify.

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Received on Mon Oct 13 2014 - 00:30:02 PDT
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