To expand on what Adrian said, you can use the "changeProtState" command in
ParmEd to set the protonation state charge vector of a Tyrosine residue to
its deprotonated value (don't forget to write out a new prmtop file with
the new charges you wanted).
The charges for these residues are taken from the constant pH parameters.
HTH,
Jason
On Mon, Apr 4, 2016 at 9:55 AM, ABEL Stephane 175950 <Stephane.ABEL.cea.fr>
wrote:
> 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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>
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>
--
Jason M. Swails
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Received on Mon Apr 04 2016 - 09:30:03 PDT
