Hi. I thought I would just 'de-lurk' to make a suggestion here :
On Thursday 27 February 2003 15:29, Tom Duncan wrote: <snip> > PS - I'm still curious about a simple way to set up an MD annealing run > on a final model without any remaining restraints from the template. Can > the developers point me to an example or guidelines in the manual?
Doesn't the 'optimize.top' script (in ${MODELLER_HOME}/examples/commands/) do something like this ? Given an initial structure (ie an initial model), local gradient descent or a variety of all-atom MD can be used via the 'OPTIMIZE' function. I'm afraid I couldn't say what default constraints might be applied, but I believe the function can be redefined (as all MODELLER functions can be) to select appropriate topologies, parameter files and ranges.
j.
Jim Procter Biomolekulare Modellierung / Zentrum Fur Bioinformatik / University of Hamburg