Acoot,
This should be very obviously laid out in the AMBER manual, which shows the
functional form of all standard AMBER force field terms, look under "Sander
Basics."
That being said, I'll answer the question as best I know how. I'm not a
force field expert, but I believe the AMBER force field (and most modern
biomolecular force fields) does not (or does not any longer) include any
explicit hydrogen bond energy terms (an exception is some of QM methods,
but that is a completely different story). All of the physics giving rise
to hydrogen bonds is implicitly encoded in the charge and Lennard-Jones
parameters.
Regards,
Brian
On Thu, May 31, 2012 at 2:40 AM, Acoot Brett <acootbrett.yahoo.com> wrote:
> Dear All,
>
> The value of the energy of the hydrogen bond has relation with distance
> and angle of the hydrogen bond related atoms. As for in the simulation
> process, the distance and angle of the hydrogen bond related atoms may
> change continuously. Will you please let me know based on which formula
> AMBER calculated the value of the energy of the hydrogen bonds?
>
> Cheers,
>
> Acoot
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>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
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Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Thu May 31 2012 - 05:00:02 PDT
