Re: It`s alive!!! [ MD without template restraints ]

[Jim Procter <procter@zbh.uni-hamburg.de>]

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