On Sat, Apr 21, 2012 at 2:38 AM, Acoot Brett <acootbrett.yahoo.com> wrote:
> Dear All,
>
> If I want to do the constant pH titration by AMBER, in which file (*.in)
> should I add the residue titration state?
The process of running constant pH simulations is detailed in the manual
(there is a chapter devoted to it). It details changing the PDB to add the
titrating residues (e.g., ASP -> AS4, GLU -> GL4, and HIS -> HIP), and how
to use the program "cpinutil.py" to build a constant pH input file. After
that, it's just like running a regular implicit solvent simulation.
> Is there any on-line tutorial or protocol on the constant pH titration by
> AMBER?
>
Not yet. It's on the to-do list.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Apr 21 2012 - 07:30:02 PDT
