[AMBER] Setting exclusions - am i overcounting ?

From: Arun Srikanth <askforarun.gmail.com>
Date: Wed, 15 Oct 2014 17:56:12 -0400

Hello amber users.

Thanks Jason and Daniel for your comments on my previous post.
I have a couple of questions that needs to be clarified.

Can you please explain the following.

In the previous post you said to *not to include *the 1-4 interaction for
the diehdrals which has M or I printed on the corner from parmed.py. But
when you look at the dihedral list (using parmed.py) the dihedrals with M
printed on the corner, the weighting factors are not zero.

They are zero only for the case in which I is printed on the corner of the
dihedral list.

So I am asking once again

1. Should we exclude 1-4 interactions for those dihedrals in which M is
printed and why does parmed.py doesn't print the scaling factors for those
dihedrals as zeros.

2. I could not find the above fact in the paper by cornell or GAFF (junmei)
, I mean the fact that excluding 1-4 pairwise interactions for certain

This is an excerpt from the paper by junmei

" Scale factors of 1/1.2 and 1/2 were applied to the 1–4electrostatic and
van der Waals interactions, respectively"

Can you please clarify this ?

Specifically daniel said if we include the 1-4 interactions for those
dihedrals, I might be overcounting.

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Received on Wed Oct 15 2014 - 15:00:02 PDT
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