AMBER Archive (2008)

Subject: Re: AMBER: Problem:neturalization

From: David Cerutti (dcerutti_at_mccammon.ucsd.edu)
Date: Thu Feb 07 2008 - 01:42:39 CST

That's going to take some degree of approximation, to be sure. If you
want, you can use Generalized Born solvent (GB, see the "igb" sander
commands) to do the simulation and that shouldn't complain about some
overall net charge on the protein (although I'm not a GB user).

To neutralize the protein without adding ions, you could mutate 9
negatively charge residues in regions that don't appear too vital to
positively charged residues. That, or mutate 18 Asp or Glu residues to
Asn and Gln, respectively (I'd actually prefer to mutate 9 Glu and Asp
residues to Lys, myself.)

Use the program SCWRL (available from the Dunbrack website at the
Fox-Chase Cancer Center, FCCC) to do the mutations.

As yet another alternative, if it's the (lack of) equilibration of
counterions you're worried about then you could solvate the system in
counterions plus a bath of 0.1M NaCl (or whatever salt matches your
counterions, I assume they'e sodium). This bath would greatly improve
(counter)ion sampling around the protein.

Dave

On Thu, 7 Feb 2008, jani sahil wrote:

> 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
> neutralization.
> 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
>
>
> Regards
> Jani Vinod
>
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