Thanks Daniel. I understand that the sum is for all the four terms of the
dihedrals.
For example lets say that I have the following dihedrals which I obtained
from parmed.py.
From your reply I understand that the sum is over 9 dihedrals and I also do
not have to count the 1-4 interaction for the last five dihedrals but if
you see the vdw and eel weighting factors from parmed it is not zero for
the fifth dihedral term (last two terms) in which M is printed. It is zero
for the the last four dihedral term as you say, which I am fine with. Why
does parmed.py does not print zero for the fifth dihedral
1 C ( c3) 9 C2 ( c3) 11 C3 ( c3) 12
O1 ( os) 0.1556 3.0000 0.0000 1.2000 2.0000
5 C1 ( c3) 30 C20 ( c3) 29 C19 ( c3) 28
O2 ( os) 0.1556 3.0000 0.0000 1.2000 2.0000
9 C2 ( c3) 11 C3 ( c3) 12 O1 ( os) 13
C4 ( ca) 0.3833 3.0000 0.0000 1.2000 2.0000
10 O ( oh) 9 C2 ( c3) 11 C3 ( c3) 12
O1 ( os) 1.1750 2.0000 0.0000 1.2000 2.0000
M 10 O ( oh) 9 C2 ( c3) 11 C3 ( c3) 12 O1
( os) 0.1440 3.0000 0.0000 1.2000 2.0000
I 13 C4 ( ca) 15 C6 ( ca) 14 C5 ( ca) 36
H10 ( ha) 1.1000 2.0000 180.0001 0.0000 0.0000
I 14 C5 ( ca) 16 C7 ( ca) 15 C6 ( ca) 37
H11 ( ha) 1.1000 2.0000 180.0001 0.0000 0.0000
I 16 C7 ( ca) 18 C9 ( ca) 17 C8 ( ca) 38
H12 ( ha) 1.1000 2.0000 180.0001 0.0000 0.0000
I 13 C4 ( ca) 17 C8 ( ca) 18 C9 ( ca) 39
H13 ( ha) 1.1000 2.0000 180.0001 0.0000 0.000
2) Which part of the paper discusses that 1-4 interactions of the improper
should not be included ? ? Can you please guide me to the paper or journal
which says this.
Thank Daniel for your help and your replies (Jason's too)
Phd student, Drexel university
Arun
On Wed, Oct 15, 2014 at 6:57 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Oct 15 2014 - 17:30:02 PDT
