AMBER Archive (2002)

Subject: Re: groups in targeted md

From: Carlos Simmerling (carlos.simmerling_at_sunysb.edu)
Date: Mon Sep 30 2002 - 09:04:26 CDT

I wrote this code, and the idea is to use RMSD as a metric
for a restraint. I'm not sure what you want to restrain- the
distance between the groups? Or do you just want each
group kept near the reference structure and only explore
relative motion? Currently the code only supports one group
but you should be able to extend it yourself.

Carlos

----- Original Message -----
From: "Christoph Brockmann" <chbrock_at_fmp-berlin.de>
To: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Monday, September 30, 2002 9:15 AM
Subject: groups in targeted md

> hello out there,
>
> has anyone found a way to use more than one group in targeted md? i can't
> see why i should not have two restrained entities moving relative to each
> other. i would like to use it for md of modelled protein complexes.
>
> regards,
> Christoph
>
> --------------------------------------------------------------------
> Christoph Brockmann
> Forschungsinstitut fuer molekulare Pharmakologie (FMP)
> Robert Roessle Str. 10
> D-13125 BERLIN, Germany
> phone: +49-30-94793-223
> email: Brockmann_at_fmp-berlin.de
> --------------------------------------------------------------------
>
>