AMBER: neutral terminals

From: Jena M <>
Date: Thu, 2 Aug 2007 01:15:46 +0100

I cut residues of a protein to create a sphere of 25 A around a ligand and I want to minimise it. I need the C- and N-terminals of the fragments in the sphere to be neutral as the minimised structure is to be used as input for Gaussian. According to some posts in the amber list the way to do this is to use protecting groups.
As the sphere has about 20 peptide fragments I need to introduce a high number of protecting groups. My question is: Does this can introduce some type of artefact in the system, such as, a change in the conformation of neighbouring residues of the capping groups? Is there another way to make the neutral terminals?
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Received on Sun Aug 05 2007 - 06:07:17 PDT
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