AMBER Archive (2005)

Subject: Re: AMBER: capping

From: John Mongan (jmongan_at_mccammon.ucsd.edu)
Date: Wed Apr 27 2005 - 11:50:43 CDT

Use the ACE and NME residues as caps. For instance

x = sequence {ACE ALA NME}

will give you a capped alanine.

I assume this is what you mean by "cap". If you actually want a
zwitterionic residue, you'll probably have to define that yourself.

John

On Wed, 27 Apr 2005 amit_at_mbu.iisc.ernet.in wrote:

> Dear amber users,
> I am doing simulation of free amino acid as a ligand in protein. I would
> like to cap the amino acid at N and C terminal. Even leap doesnt include
> missing hydrogen atom at the N terminal.Give me some suggestion how to
> perform capping in amber. I am a new amber user. Any suggestion is
> appreciated.
>
> Thanks.
>
> amit
>
>
>
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