AMBER Archive (2008)

Subject: AMBER: Problem:neturalization

From: jani sahil (
Date: Wed Feb 06 2008 - 23:03:35 CST

Dear All,
I want to simulate an Aspartic protease
As it is a acid protease it has a charge of -18.0
I am using Amber for simulation.
I was able to run simulation for the protein where I used counter ions for
Sir now I need to simulate the protein by neutralizing the protein without
adding any ions
Sir can you suggest me how can I go about to neutralize the protein without
adding any ion.

Thanking you in Anticipation

Jani Vinod

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