Re: [AMBER] MD simulations of deprotonated tyrosine residue with AMBER

From: ABEL Stephane 175950 <Stephane.ABEL.cea.fr>
Date: Mon, 4 Apr 2016 13:55:55 +0000

Thanks Adrian,

I will take a look of these files

Stephane

________________________________________
De : Adrian Roitberg [roitberg.ufl.edu]
Envoyé : lundi 4 avril 2016 15:31
À : AMBER Mailing List
Objet : Re: [AMBER] MD simulations of deprotonated tyrosine residue with AMBER

Hi Stephane.

You could try constant pH simulations, but if you are sure the tyrosine
is deprotonated at the pH of your simulation, you can just change the
charge set for the atoms.

Look at the constant pH files and you will find the charge vector for
deprotonated tyrosine there.

adrian


On 4/4/16 9:22 AM, ABEL Stephane 175950 wrote:
> Hello Amber Users,
>
> I am interested to perform MD simulations with a peptide that contains a deprotonated tyrosine residue. Does somebody know where I can find these (rare) topology/param for this residue?
>
> Thanks
>
> Stéphane
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber 

--
Dr. Adrian E. Roitberg
Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Mon Apr 04 2016 - 07:00:05 PDT
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