Re: [AMBER] pH dependent calculation for Oligomers

From: Jason Swails <>
Date: Mon, 4 Jan 2016 06:02:46 -0500

On Mon, Jan 4, 2016 at 5:19 AM, Mijiddorj Batsaikhan <>

> Dear all,
> Hello, I want to make pH dependent simulation of dimer, trimer and pentamer
> structure of a peptide. How to make it?

​The two general approaches are to fix protonation states appropriate for
each pH you want to simulate and run separate simulations or to use
constant pH molecular dynamics where the protonation states can change as a
function of pH.

Which one you should choose depends on what you are trying to learn and the
nature of your system. It may be worth trying both.

> ​​
> Can I use H++ server for oligomers?

​I believe so. Have you tried it? Do the results seem reasonable?


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Jan 04 2016 - 03:30:03 PST
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