Hi Adrian,
thank you for you're suggestion.
I am not sure what you mean by "I think concentration cans be adjusted
up to 0.1M, can you clarify ?
>> Is it possible to run explicit contant pH MD simulation with above 0.1M NaCl concentration?
If you want to keep the tyrosines in the deprotonated state and NOT
aloow them to change, then all I wrote above does not matter. Al you
need to do is set up a constant pH calculation with those tyrosines
treated as titratable, then start the simulation in the deprotonated
state, and set the input so you never try to change the protonation state.
>> Can I specifically mention which Tyr-X I want to keep in deprotonation state? Ones I have generated the cpin file, should the "RESSTATE" be changed accordingly to have a -1 charge?
Can you please guide me to a tutorial/article which explains this in more detail.
Thanks
Regards
Sowmya
________________________________________
From: Adrian Roitberg [roitberg.ufl.edu]
Sent: Friday, August 18, 2017 5:38 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Deprotonation of Tyr
Hi Sowmya
I am not sure what you mean by "I think concentration cans be adjusted
up to 0.1M, can you clarify ?
The constant pH calculation you might want uses a reference compound,
tyrosine in solution, which is done at some level of ionic strength. Fo
r the most part, ionic strength has a VERY minor role in changing pKas,
but if you think you need to adjust this, you need to change the
reference free energy in cpin to reflect the pka of tyrosine in solution
at the new ionic strength.
If you want to keep the tyrosines in the deprotonated state and NOT
aloow them to change, then all I wrote above does not matter. Al you
need to do is set up a constant pH calculation with those tyrosines
treated as titratable, then start the simulation in the deprotonated
state, and set the input so you never try to change the protonation state.
It is a bit of a hack, but it is exact.
adrian
On 8/18/17 9:24 AM, Sowmya Indrakumar wrote:
> Dear All,
> I wish to perform simulations with varying salt concentration of NaCl of upto 200mM at a particular pH=7. I want to keep some of the Tyrosines in the deprotonated state.
>
> So here, my question is, Can I perform these simulations using constant pH MD? Because, I think concentrations can be adjusted to upto 0.1M.
>
> Is there any other way to consider doing the deprotonation?
> Kindly, give me you're suggestion in this regard.
> Regards
> Sowmya
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
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 Fri Aug 18 2017 - 09:00:06 PDT
