Re: amber-developers: Question concerning wildcards in dihedral definitions.

From: Carlos Simmerling <>
Date: Tue, 28 Jun 2005 20:17:25 -0700

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.

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
>[a little more blathering on the previous subject]:
>My recollection is the opposite: overriding should only happen if both
>atoms _and_ the periodicity of the specific torsion match the wild-card
>This is certainly the way frcmod changes work: a frcmod file change only
>supplants and exact match (including periodicity) in the main parameter
>This all goes back to the question (which was embedded in early versions
>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
>treated more like several terms (which came into the code when
>issues were dominant.)

Carlos L. Simmerling, Ph.D.
Associate Professor           Phone: (631) 632-1336
Center for Structural Biology Fax:   (631) 632-1555
Stony Brook University        Web:
Stony Brook, NY 11794-5115    E-mail:
Received on Wed Apr 05 2006 - 23:49:55 PDT
Custom Search