I'm with Tom, I recall (at least in Peter's group) the understanding
that multiple terms were a set to be replaced if the atoms matched.
I would think that the generics don't usually adjust relative energies but
instead are for barriers, in that case it probably isn't horribly wrong
if it's done the wrong way (whichever that is).
I guess the key is knowing if the person included the generic when
the fitting was done (in the MM to match the QM profile). I would
guess that removing the generic from the MM calc would be an
extra step (making a specific with all terms zero) so I think it's
likely that you're right, the generics get kept. Certainly we all should
know how to code works so that we all do the same thing as leap
(and each other) in developing new parameters.
carlos
David A. Case wrote:
>On Tue, Jun 28, 2005, Thomas E. Cheatham, III wrote:
>
>
>
>>but my recollection which is likely flawed is that if a specific
>>torsion is present, it overrides the general (wildcards), independent of
>>periodicity...
>>
>>
>
>[a little more blathering on the previous subject]:
>
>My recollection is the opposite: overriding should only happen if both
the
>atoms _and_ the periodicity of the specific torsion match the wild-card
one.
>
>This is certainly the way frcmod changes work: a frcmod file change only
>supplants and exact match (including periodicity) in the main parameter
file.
>This all goes back to the question (which was embedded in early versions
of
>the code) of whether a torsion term with multiple Fourier components is a
>single entity (as it was in very early versions of Amber), or whether it
is
>treated more like several terms (which came into the code when
vectorization
>issues were dominant.)
>
>...dac
>
>
>
--
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
===================================================================
Received on Wed Apr 05 2006 - 23:49:55 PDT
