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