Re: [AMBER] question about bond command

From: Philippe Pinard <>
Date: Sat, 24 Jul 2010 17:13:45 -0700 (PDT)

Thanks. for this my whole macromolecule is neutral now if i add ions it is going
to be charged!! will amber accept calculations with a total charge different
from zero? I used addions before in another work when my protein charge was
different from zero example addions 8 Na+.

In this specific case, there seems to be a need to protonate or something like
this for say pH=5. How can I do this since my molecule is already built. And how
to know if I am at low pH, or high pH?

From: Bill Ross <ross.cgl.ucsf.EDU>
Sent: Sat, July 24, 2010 9:57:32 PM
Subject: Re: [AMBER] question about bond command

> I want to perform calculations at specific pH. How do I do this in Amber?

You must calculate the number of ions to use for the box of water
you will create, and add them with leap's addions command after
solvation. There is no way to simply request a pH.


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