Re: [AMBER] Avoid pH Titration of LYS and TYR

From: Adrian Roitberg <roitberg.ufl.edu>
Date: Wed, 27 Sep 2017 15:48:29 -0400

Hi

If you are really new to MD, then jumping into constant pH right away
might not be a great idea. You need some experience for that.

As for your questions for LYS/TYR, it really depends on your system and
your pH range.

What we usually do is run short simulations (but long enough to see
something), check out the protonation states, and if we see that the LYS
stayed charged then we delete it from hte set of titratable residues.

Adrian


On 9/27/17 3:17 PM, R zu wrote:
> Hi. I am quite new to running MD simulations, and haven't ran any constant
> pH simulation before.
>
> Is it a good idea to avoid titrating lys residues and some tyr residues?
> I hope that would give me a simulation with less unnecessary solvent / side
> chain reorganization.
>
> Are there any common artifacts in constant pH simulations?
>
> Thank you.
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-- 
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Wed Sep 27 2017 - 13:00:03 PDT
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