Re: AMBER: how to neutralize the peptide

From: Joseph Nachman <nachman.hera.med.utoronto.ca>
Date: Wed, 27 Oct 2004 13:04:50 -0400 (EDT)

Hello -

Leap has parameters for neutral (protonized) ASP and GLU: ASH and GLH
resepctively, and neutral LYS: LYN. Another way to neutalize the peptide
is to add counterions.

Good luck,

Joseph

 On Wed, 27 Oct 2004, Ye Mei wrote:

> Dear Amber users
>
> Could anyone tell me how to neutrolize the peptide in leap.
> By default, leap adds charges to terminals and some sidechains. But I need neutralized peptide and force field parameters for each atom.
> Can anyone give any help?
>
>       
>
> Best regards,
>
> Ye Mei
> ymei.itcc.nju.edu.cn
> 2004-10-27
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Joseph Nachman				Department of Biochemistry
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fax: +1 416 978-8548			Canada
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Received on Wed Oct 27 2004 - 17:53:01 PDT
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