On Mon, Apr 12, 2004 at 05:29:48PM -0400, Thomas Duncan wrote:
> I'd like to confirm the default and options for dynamic restraints.
>
> I believe the default is set, under the OPTIMIZE command, as DYNAMIC_SPHERE
> = on
> (all others off) and that this means that only soft-sphere overlap
> restraints are generated.
That's correct.
> Are all the other DYNAMIC_ options available (LENNARD, COULOMB, MODELLER,
> ACCESS)
Yes, although no derivatives are calculated for DYNAMIC_ACCESS
restraints, so their use in optimization is limited.
> and, specifically, what type of nonbonded restraints are included if
> DYNAMIC_MODELLER is turned on?
These are dynamic restraints defined in a restraints file. See
http://salilab.org/modeller/manual/node98.html
These are most commonly used for implementing the statistical potential
used for loop modeling (see modlib/melo1-dist.lib and Melo, F. and
Feytmans, E. (1997), J. Mol. Biol. 267 p207).
Ben Webb, Modeller Caretaker
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