Re: AMBER: Sample more conformational space

From: Marc Baaden <>
Date: Wed, 02 Mar 2005 14:03:02 +0100


if computer time is not an issue, you might want to think about a
replica-exchange type approach. Some people have also combined this
with an implicit solvent approach in which case it becomes computationally
more efficient.

Best wishes,

>>> Bogos Agianian said:
>> Dear Amber users,
>> Starting from a crystal structure of a protein-peptide complex, I try to mo
>> the binding of the same peptide to very similar isoforms of the protein
>> (created by homology modeling). The starting structure of the peptide is th
>> one obtained after 3D-superposition of the homology models onto the crystal >> structure of the complex.
>> My question is what is a good protocol in Amber 7.0 to sample as much
>> conformational space of the peptide as posible so that it gets un-stuck of
>> conformation in the crystal.
>> ..but the peptide is not moving a lot. Is there a good way to give it a
>> kick?

 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris      -
 FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217
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Received on Wed Mar 02 2005 - 13:53:01 PST
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