AMBER Archive (2005)

Subject: Re: AMBER: Can constant pH be used for minimization?

From: John Mongan (jmongan_at_mccammon.ucsd.edu)
Date: Tue Jun 14 2005 - 19:03:38 CDT


As Dave mentioned, constant pH sampling is for MD only -- it doesn't
make sense during minimization since changing the protonation state
would move the minimum around. However, as a convenience, the constant
pH code can be used to set the protonation state of a molecule prior to
minimization. This may be useful if you're planning to start your MD
with a protonation state representing very acidic or very basic
conditions and want to minimize based on this initial state.

John

Kenley Barrett wrote:
> Dear Amber users,
>
> I just did a minimization of a large protein in which I tried to run
> constant pH; the minimization appeared to work fine but the .cpout
> file was empty and the .cprestrt file was never generated. Is constant
> pH for molecular dynamics runs only?
>
> Thanks for your help,
> Kenley
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