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
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Zunnan Huang Tel: 405-325-9629(Home)
533B, Sooner Dr. 405-325-5159(Lab)
Norman, OK 73072 405-249-3296(Cell)
Email: znhuang.chemdept.chem.ou.edu; znhuang.ou.edu
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Received on Fri May 09 2003 - 21:53:01 PDT
