# Re: [AMBER] Setting exclusions - am i overcounting ?

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Wed, 15 Oct 2014 16:57:55 -0600

Hi,

Since I'm not 100% clear on exactly what you're trying to calculate,
I'll try to give an overview.

There are 3 energy terms associated with the dihedral-related topology
parameters: dihedral, 1-4 electrostatic, and 1-4 van der Waals. The
dihedral energy is calculated over all dihedral terms:

Edih = SUM[ Pk * (1.0 + cos(Pn * phi - Phase)) ]

The 1-4 electrostatic/vdW terms are calculated over only the dihedral
terms that are not improper (4th atom index negative) or "end" (3rd
atom index negative). So say for example you have 4 dihedral terms:

1: D1
2: D2
3: D3 I
4: D4 E

The dihedral energy summation would be done over all 4 dihedrals, but
the 1-4 electrostatic and vdW sums would only use the first and fourth
atoms of D1 and D2, hence the scaling factors will only matter for D1
and D2.

Hope this helps,

-Dan

On Wed, Oct 15, 2014 at 3:56 PM, Arun Srikanth <askforarun.gmail.com> wrote:
> 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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Department of Medicinal Chemistry
University of Utah
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http://home.chpc.utah.edu/~cheatham/
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Received on Wed Oct 15 2014 - 16:00:03 PDT
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