Re: conformational sampling

From: Carlos Simmerling <>
Date: Thu 23 Jan 2003 18:45:58 -0500

there isn't any automated way in AMBER to build different
conformations for the copies. We have often used high
T with restraints on some regions in order to force the
copies to adopt alternate structures. I also have a utility
program on the moil-view site (,
look at the bottom for Carlos's undocumented AMBER analysis program).
It will allow you to combine multiple single-copy coordinate sets into
a LES coordinate set. It will also split LES coordinates or trajectories
into multiple single-copy files, or average the copies into a single-copy
I hope that helps.

----- Original Message -----
From: "Robert G. Endres" <>
To: <>
Sent: Thursday, January 23, 2003 9:17 AM
Subject: conformational sampling

> Dear AMBER users,
> for locally enhanced conformational sampling, one can use the module
> ADDLES and subsequently sander.LES which allows an ensamble of the system
> to evolve independently and so can sample more conformations.
> Since the "copies" seem to start out with the same coordinates, does
> anyone know if and how one can choose different initial coordinates, like
> different rotamers of an amino acid side chain? Or, can one specify and
> automate a range - lets say of dihedral angles - to start out with?
> Any suggestions are welcome! Thanks.
> -Robert
Received on Thu Jan 23 2003 - 15:45:58 PST
Custom Search