AMBER Archive (2004)

Subject: Re: AMBER: pH effect on protein folding

From: Bimo Ario Tejo (bimo7_at_gmx.de)
Date: Thu Jul 15 2004 - 22:34:39 CDT

Rukman,

Use Amber8; it's able to do MD simulation in constant pH...(page 151, Users'
Manual).

If you use previous version of Amber, you have to calculate pKa value of
each residue in your protein at different pH. TITRA would be able to do this
task for you.

Best wishes,
Bimo

> Hi,
>
> I am planning to do study the effect of pH on protein folding by MD
> simulation. But the problem is how to include such pH effect to the force
> field? Any suggestion will be appreciated.
>
> Thanks
>
> Rukman
>
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