AMBER Archive (2000)

Subject: Does AMBER include effects from pH?

From: Lawrence Tsang (bchlawrence_at_cuhk.edu.hk)
Date: Tue Jul 11 2000 - 02:24:09 CDT

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