AMBER Archive (2007)

Subject: Re: AMBER: problems in adding ACE and NME group

From: David A. Case (case_at_scripps.edu)
Date: Thu Jun 21 2007 - 00:10:43 CDT

On Thu, Jun 21, 2007, backy wrote:

> If there is a need in placing the whole ACE and NME group, how should I
> input their initial coordinations?

This is a very rare thing to do, and Amber admitedly doesn't make it very
easy. It isn't something I would recommend just "for practice".

You might use a homology-modeling program to add alanine at both ends, then
delete the atoms you don't need, and change the residue names to ACE and
NME.

....dac

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