AMBER Archive (2005)

Subject: RE: AMBER: Dihedral Energy calculation

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Mar 02 2005 - 10:48:56 CST

Dear Yen

> "On the other hand, if n is a positive number, the
> followed term is for another torsional angle" is not
> clear can you please ellaborate.
> hc-c3-c -o 1 0.80 0.0 -1.
> Junmei et al, 1999
> hc-c3-c -o 1 0.08 180.0 3.
> Junmei et al, 1999

If I understand what you are asking it concerns why one torsion angle has a
-ve term and one does not. This is due to the way the torsion angles are
used internally in the code. Amber scales 1-4 nonbond interactions by scee
and scnb and thus requires a list of 1-4 interactions. To calculate this
list on every step would be very expensive but fortunately one already
exists in the form of the dihedrals terms. However, it is possible to have
more than one dihedral term for a given set of atoms and so the 1-4n
non-bond code needs a way to avoid counting each 1-4 non bond interaction
more than once. This is done by marking the first torsion angle's n value as
positive and the rest negative. The code for scaling the 1-4 interactions
then simply only considers dihedral terms that have +ve n values and so
avoids the problem of over counting. I hope this makes sense. In terms of
the actual dihedral terms the -ve sign makes no difference to the
calculation.
 
> The torsions H1-C4-C5-O6, H2-C4-C5-O6, H3-C4-C5-O6
> are
> of the same type but Amber is reporting H2-C4-C5-O6
> two times and the rest 3 times in the topology file.
> I am trying to calculate the same. Therefore I need to
> understand how this is done in amber.

I'm not quite sure what you mean here, can you list the terms as they appear
in the prmtop file.

All the best
Ross

/\
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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
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