Re: It`s alive!!! [ MD without template restraints ]
To: Modeller_Usage <>
Subject: Re: It`s alive!!! [ MD without template restraints ]
From: Jim Procter <>
Date: Thu, 27 Feb 2003 17:03:24 +0100
Organization: Zentrum Bioinformatik Hamburg
Reply-to:
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