Re: [AMBER] how to neutralize protein when using intrinsic water model

From: David A Case <>
Date: Mon, 14 Nov 2016 11:22:34 -0500

On Mon, Nov 14, 2016, Thakur, Abhishek wrote:
> I am trying to simulate my protein with intrinsic water model (GB/SA),
> but I am confused how to neutralize my protein?

One generally does not explicitly neutralize proteins when using GB models.
The models have been parameterized without use of any explicit ions.

Various people have explored other approaches, but these are really testing
out new force field ideas. Others on the list may wish to chime in with their
experience here. But my personal view is this: if explicit ions are crucial
to getting good results, you should be using explicit waters as well.


AMBER mailing list
Received on Mon Nov 14 2016 - 08:30:05 PST
Custom Search