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
dihedrals.
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.
Thanks
Arun
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Received on Wed Oct 15 2014 - 15:00:02 PDT
