AMBER Archive (2004)

Subject: Re: AMBER: how to neutralize the peptide

From: Joseph Nachman (nachman_at_hera.med.utoronto.ca)
Date: Wed Oct 27 2004 - 12:04:50 CDT

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_at_itcc.nju.edu.cn
> 2004-10-27
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