AMBER: Work with constand pH

From: tri nam Vo <>
Date: Wed, 25 Apr 2007 01:13:05 -0700 (PDT)

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).

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Received on Sun Apr 29 2007 - 06:07:04 PDT
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