AMBER Archive (2007)

Subject: Re: AMBER: Work with constand pH

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Wed Apr 25 2007 - 08:49:59 CDT

As you have read, you'll use GB implicit solvent model.
Don't solvate (neutralize) your protein, and follow the example in the manual.

On 4/25/07, tri nam Vo <mouseelephant2002_at_yahoo.com> wrote:
> Dear Amber user,
> I'm using Amber8. I'd like to make MD on protein at some pH.
> I've 2 questions:
> First, Is it necessary to solvate my molecule and addion to neutral it? I
> used 'charge' command and know that the total charge is 0.9989 and I don't
> how to neutral it with 'addions2' command. Can someone help me?
> Second, I've read the amber8 manual, it said that use igb = 2, cut = 30
> ...If it's necessary to solvate my molecule, how can I change these value ?
> (It seem that igb only work without solvate).
> Thanks.
>
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> 

-- 
Best wishes,

MYUNGGI YI
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