[MMTK] H-bond questions

[Konrad Hinsen]

Kyle Krull <krullk@purdue.edu> writes:

> 1. Does MMTK have a built in way to detect if a hydrogen bond is present
> between two Residues?  I have not seen any mention of a function

No. One reason is that I don't know either how this is usually done.

> Maybe partial charges should be considered?  I think MMTK already has
> partial charges assigned from the dictionary.

Yes, but partial charges are a property of a force field, not an
intrinsic property of atoms and molecules. So if your method relies on
partial charges, it will work only in a universe with an assigned
force field that defines charges.

> 2. Does MMTK's implementation of AMBER include hydrogen bonds (in
> addition to van der Waals, electrostatics, etc...)?  If this isn't

Amber 94 does not have any hydrogen bond terms, therefore the answer
is no.

Konrad.
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