Re: [AMBER] Accelerated md for protein dna complex with modified residue

From: Vlad Cojocaru <>
Date: Wed, 15 Jul 2015 15:11:13 +0200

Accelerated MD can be performed in any setup you used for classical MD.
As with all MD-based methods, running multiple, reasonably-long
trajectories is usually recommended. Whether you see or not
conformational changes it depends on the system and on the time scale of
the changes you study .... Of course, force field-dependence of
transitions and timescales is always possible.

Hope they help

On 07/14/2015 08:05 PM, Muthukumaran R wrote:
> Dear amber users,
> I am working on a protein dna complex with an acetylated lysine. I have
> generated the parameters for acetyl-lysine using resp.. I have performed
> all-atom simulations, but visualize comformational change which is reported
> to occur at large time scale..
> My complex is very large (1064 residues) and to sample larger timescale by
> conventional md is not possible. So i would like to use accelerated md.
> My queries are:
> 1. Is it possible to perform acemd with modified residues?
> 2. Is ff99sb force field compatible for acemd of a protein dna complex?
> 3. Is it necessary to generate multiple trajectories from acemd to see the
> conformational changes?
> _______________________________________________
> AMBER mailing list

Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]
AMBER mailing list
Received on Wed Jul 15 2015 - 06:30:03 PDT
Custom Search