AMBER Archive (2003)

Subject: Re: What kind of interactions are ignored for end group interactions

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Fri May 09 2003 - 16:07:26 CDT

I'm not positive what section you're quoting, but it
sounds like the 1-4 vdw and electrostatic interactions.
there are calculated from the dihedral list. since
some rotatable bonds have multiple dihedral terms, you
don't want to calculate 1-4 for that set of atoms multiple
times, only for the first dihedral involving them. also, in
rings you might not want to count them at all, or there may
be other dihedrals for the same 1-4 atoms (such as in a
6-member ring, the same 1-4 atoms are in 2 different bond
rotation terms).

Is that what you wanted to know?
Carlos

----- Original Message -----
From: "Huang Zunnan" <zn_huang_at_yahoo.com>
To: <amber_at_heimdal.compchem.ucsf.edu>
Cc: <znhuang_at_chemdept.chem.ou.edu>
Sent: Friday, May 09, 2003 4:41 PM
Subject: What kind of interactions are ignored for end group interactions

> Dear Sir or Madam:
>
> In Amber File Specifications, it is said that "End
> group interactions are ignored, for example, in
> dihedrals of various ring systems (to prevent double
> counting) and in multiterm dihedrals." I could not
> understand this. At my first thought, torsions energy
> and torsions forces are not calculated for those end
> group interations, because the last torsion, for
> example, in dihedrals of various ring system is not
> independent in order to keep the ring planar. Second
> thought, 1-4 (elec. and vadw) interations are not
> calculated for those atoms connected in end group
> interations. I tested these two situation but it
> seemed both did not give the right answer. I would
> really appreciate if someone can help me to understand
> the end group interactions to be ignored.
>
> Sincerely yours
> Zunnan Huang
>
> =====
> /***********************************************
> Zunnan Huang Tel: 405-325-9629(Home)
> 533B, Sooner Dr. 405-325-5159(Lab)
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