Re: [AMBER] End of protonate method with amber11?

From: Guenegou, Guillaume [ORDFR] <GGUENEGO.ITS.JNJ.com>
Date: Tue, 26 Apr 2011 16:33:22 +0200

Ok thanks, I understood this time !


-----Original Message-----
From: Ben Roberts [mailto:ben.roberts.geek.nz]
Sent: mardi 26 avril 2011 16:22
To: AMBER Mailing List
Subject: Re: [AMBER] End of protonate method with amber11?

Hi Guillaume,

On 26/04/2011, at 10:12 AM, Guenegou, Guillaume [ORDFR] wrote:

> I understand I can use the old protonate program, but the goal is to
> use
> amber11 and only amber11.
> So I cannot use this old program anymore. Is there any substitution
> method?

If you want to add hydrogen atoms, the new method is "reduce". It's the
name of a program, like "tleap".

> I don't understand what you mean by "reduce code". Is it a new way to
> make protonate?

If I recall correctly, "protonate" was removed from Amber 11
distributions because its functionality was already provided by
"reduce".

Hope that helps,
Ben

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Received on Tue Apr 26 2011 - 08:00:02 PDT
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