AMBER Archive (2007)

Subject: Re: AMBER: Work with constand pH

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Fri Apr 27 2007 - 20:42:32 CDT

Read the following paper, and you'll get some idea.

You set all values for contant pH simulation even in minimization,
but the protonation state will be changed only during MD simulation,
not in minimization.

175aa, more important thing is how many titrable sites you have.
If you have more, you need to increase the MC frequency (or longer simulation).
According to the paper, 1ns is enough for 10 titrable sites.

J. Mongan, D.A. Case and J.A. McCammon
Constant pH molecular dynamics in generalized Born implicit solvent
J. Comput. Chem. 25, 2038-2048 (2004)

On 4/26/07, tri nam Vo <mouseelephant2002_at_yahoo.com> wrote:
> Dear Myunggi,
> I'm still confused. The manual just say too simple, is there any tutorial
> which more detail?(I've just read the manual amber8.pdf part 5.19)
> I've some questions: should we include cipn file when run minimization by
> -cpin flag ? In that case, should we set value for icnstph and solvph
> parameters in min.in file?
> And which value is suitable for nstlim? My protein have 175aa.
> Thanks a lot.
>
> Myunggi Yi <myunggi_at_gmail.com> wrote:
> As you have read, you'll use GB implicit solvent model.
> Don't solvate (neutralize) your protein, and follow the example in the
> manual.
>
>
>
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>
> 

-- 
Best wishes,

MYUNGGI YI
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