On Wed, Oct 15, 2014 at 8:05 PM, Arun Srikanth <askforarun.gmail.com> wrote:
> 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
>
All ParmEd prints is *exactly* what is in the prmtop file. If there is an
M or I next to it (as ParmEd prints it -- E or I as cpptraj/rdparm prints
it), you do not count those 1-4 nonbonded interactions. Period. The
scaling factors become irrelevant. I see what is confusing you, but this
is simply an implementation detail that you can only know if you understand
the history behind the scaling factors defined in the prmtop file or have
heard somebody that knows this history describe it before. I've given my
explanation in the postscript, since it is long. [1]
> 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.
>
Look at the definition of an improper torsion. It involves a central atom
that is bonded to every *other* atom. As a result, every atom in the
improper forms either a bond *or* an angle with every other atom in the
improper. And bonds and angles are completely excluded by the Amber force
field. This isn't a case of impropers being treated "specially" -- it's a
case of the bond- and angle- exclusions taking precedence (as they always
do).
HTH,
Jason
[1] So the scaling factors are the quantities by which the 1-4 nonbonded
terms are *divided* to get the actual interaction. When the scaling
constant is set to 0, this term becomes infinite. There are some torsion
terms defined in the dihedral whose end groups are ALWAYS excluded --
specifically the first N-1 terms of an multi-term torsion with N terms (so
you only count the 1-4 nonbonded interactions for the N'th term). If you
set these scaling factors to 0 and some code actually (erroneously)
computes the 1-4 nonbonded interactions for that torsion term, your energy
and forces will become infinite. It's a way of making sure that a buggy
program blows up rather than spits out reasonable (but still very *wrong*)
answers.
However, there are certain torsion parameter types for which the end groups
are excluded in some specific torsions, but are not excluded for other
torsions. This happens specifically in systems containing a 4-, 5-, or
6-membered ring. For the purpose of this explanation, only consider atoms
_in_ the ring. In a 4-membered ring, atoms that are 1-4 to each other are
also bonded to each other. In 5-membered rings, atoms that are 1-4 are
also angled to each other. In 6-membered rings, atoms that are 1-4 to each
other are 1-4 to each other through a *different* set of 3 bonds. Draw out
examples to convince yourself that what I said was true. In this case,
some of the torsions defined here must be defined as "M" (or "E") to make
sure that their "end-group interactions" (i.e., 1-4 nonbonded terms) are
omitted, since they are either already excluded by bond or angle terms, or
they're already included by *another* torsion term. However, since the 4
atom types defined in that torsion *may* be used elsewhere in your
molecule, you need to make sure that the nonbonded scaling factors for that
parameter is "correct".
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Oct 15 2014 - 18:00:03 PDT
