AMBER Archive (2003)

Subject: Re: conformational sampling

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Thu Jan 23 2003 - 17:45:58 CST

Robert,
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 (morita.chem.sunysb.edu/mlv.html,
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
file.
I hope that helps.
Carlos

----- Original Message -----
From: "Robert G. Endres" <endresrg_at_ornl.gov>
To: <amber_at_heimdal.compchem.ucsf.edu>
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
>
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