Re: AMBER: Amber 8: heterogeneous multiple copy LES method

From: Carlos Simmerling <>
Date: Thu, 14 Jul 2005 17:17:07 -0400

the current code is not set up to do that. Older versions
of Amber had something called "chemical monte carlo" that
may do what you want. I think that what you want could
be done if you're willing to change the code, but there are
a few things to consider. For one, since the non-LES atoms
interact with the average energy/force felt between them
and each of the LES copies, you might have steric problems.
For example, if you did Phe and Ser, the other groups would bump
into the Phe ring before they could get close enough to
H-bond to the Ser hydroxyl. Same for Phe and Trp, the Phe
will be in space big enough to hold Trp and the other atoms
could not pack with it.There could be ways to get around that,
but it's a challenge. As far as code changes go I think all that
you need is a program that could make prmtops, the actual
MD code should be fine as it stands if your prmtop is
in standard LES style. Check the Amber web page for
details on the format, you could use the addles program
as a guide. I think that part is easier than the steric problem.

Angela Liu wrote:

>Dear Amber users,
>The LES program in Amber 8 can do homogeneous multiple
>copy (i.e. same chemical fomula but with different
>conformation). Let's say I want to create a peptide
>chain in which one residue is a heterogeneous multiple
>copy of several different amino acids. For example,
>one residue can be 50% phenylalanine and 50%
>tryptophan (both are aromatic). Similar or different
>multiple copies can exist for different residues.
>What do I need to change to create a proper topology
>file for such multiple copies?
>Thank you very much for your insight and help!
>Do You Yahoo!?
>Tired of spam? Yahoo! Mail has the best spam protection around
>The AMBER Mail Reflector
>To post, send mail to
>To unsubscribe, send "unsubscribe amber" to

Carlos L. Simmerling, Ph.D.
Associate Professor           Phone: (631) 632-1336
Center for Structural Biology Fax:   (631) 632-1555
Stony Brook University        Web:
Stony Brook, NY 11794-5115    E-mail:
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Thu Jul 14 2005 - 22:53:00 PDT
Custom Search