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.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.
>
> ________________________________
> Ahhh...imagining that irresistible "new car" smell?
> Check out new cars at Yahoo! Autos.
>
>
--
Best wishes,
MYUNGGI YI
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306
Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi
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Received on Sun Apr 29 2007 - 06:07:07 PDT
