AMBER Archive (2000)

Subject: Re: Does AMBER include effects from pH?

From: Kouji Hayama (hayama_at_lance.mecha.osakafu-u.ac.jp)
Date: Wed Jul 12 2000 - 02:40:23 CDT

Hello,

I am also interested in ph on amber.
I also want to know how to use ph on amber.

Thank you.

Lawrence Tsang wrote:
>
> Hello,
>
> I've homology modelled a protein from MODELLER.
> No H atoms is included.
>
> Then when I subject it to AMBER for MD, can I choose
> what pH in that simulation?
>
> Because under different pH, the individual AA may "feel"
> different environment.
>
> Can one tell how to calculate the ionization state for each residue
> under different pH?
>
> Thanks!
>
> Lawrence Tsang
> Dept of Biochemistry
> The Chinese University of Hong kong