Only if you want them to titrate. If you think they'll stay in their
ionized forms at the pH ranges you plan to probe, you can likely leave them
as ASP and GLU (although continuing to titrate histidine will likely give
you a better sampling of the HID/HIE tautomeric states).
HTH,
Jason
On Sat, Oct 30, 2021 at 3:21 PM Divya Rai <drai550.gmail.com> wrote:
> Okay, thank you.
> And since I am using a basic solvent pH, do I need to still change the
> names of the acidic residues to their titrable names?
>
>
> ---------- Forwarded message ---------
> > From: <amber-request.ambermd.org>
> > Date: Sat, Oct 30, 2021 at 12:30 AM
> > Subject: AMBER Digest, Vol 3526, Issue 1
> > To: <amber.ambermd.org>
> >
> >
> >
> > Message: 6
> > Date: Fri, 29 Oct 2021 19:49:15 +0530
> > From: Divya Rai <drai550.gmail.com>
> > To: amber.ambermd.org
> > Subject: [AMBER] Constant pH MD simulation
> > Message-ID:
> > <
> > CAG8dHqQcJP9iNfUEXD11xCE8Fj-nAOLovpP6LPg7JrEMqR3++Q.mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Hello everyone,
> >
> > I have been trying to carry out a constant pH MD simulation using AMBER
> 18
> > with the help of the "Amber Advanced tutorial 18" for the first time.
> > However, for my system I now need to titrate CYS, LYS and TYR residues
> and
> > for which I need to know the titrable residue name of each which is not
> > mentioned in the tutorial.
> > I'd really appreciate it if anyone could help me out with this.
> >
> >
> > *Regards,*
> >
> > *Divya Rai*
> >
> > *Research Scholar*
> >
> > *Department of ChemistryIndian Institute of Technology, Kharagpur*
> >
> >
> > ------------------------------
> >
> > Message: 7
> > Date: Fri, 29 Oct 2021 11:22:21 -0400
> > From: Jason Swails <jason.swails.gmail.com>
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: Re: [AMBER] Constant pH MD simulation
> > Message-ID:
> > <
> > CAEk9e3rB+onw-_eweDvSob434KsZWgexWTNamsjwLDfep8mv2Q.mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > CYS, LYS, and TYR are, themselves, the titratable residue names for
> > cysteine, lysine, and tyrosine. cpinutil should recognize those residues
> > and support creating input files titrating those residues.
> >
> > HTH,
> > Jason
> >
> > On Fri, Oct 29, 2021 at 10:19 AM Divya Rai <drai550.gmail.com> wrote:
> >
> > > Hello everyone,
> > >
> > > I have been trying to carry out a constant pH MD simulation using AMBER
> > 18
> > > with the help of the "Amber Advanced tutorial 18" for the first time.
> > > However, for my system I now need to titrate CYS, LYS and TYR residues
> > and
> > > for which I need to know the titrable residue name of each which is not
> > > mentioned in the tutorial.
> > > I'd really appreciate it if anyone could help me out with this.
> > >
> > >
> > > *Regards,*
> > >
> > > *Divya Rai*
> > >
> > > *Research Scholar*
> > >
> > > *Department of ChemistryIndian Institute of Technology, Kharagpur*
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > --
> > Jason M. Swails
> >
> >
> > ------------------------------
> >
> > Message: 8
> > Date: Fri, 29 Oct 2021 15:24:22 +0000
> > From: Vinicius Wilian Cruzeiro <vwcruz.stanford.edu>
> > To: "amber.ambermd.org" <amber.ambermd.org>
> > Subject: Re: [AMBER] Constant pH MD simulation
> > Message-ID:
> > <
> >
> MWHPR0201MB3547A90482E6BA448E780F33A8879.MWHPR0201MB3547.namprd02.prod.outlook.com
> > >
> >
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Hello Divya,
> >
> > The titratable residue names of these residues are CYS, LYS, and TYR. I
> > suggest you also take a look at this nice tutorial:
> > http://jswails.wikidot.com/explicit-solvent-constant-ph-md
> >
> > Best,
> >
> > Vin?cius Wilian D. Cruzeiro, PhD
> > Postdoctoral Researcher
> > Department of Chemistry
> > Stanford University
> > Twitter: .vwcruzeiro
> > ________________________________
> > From: Divya Rai <drai550.gmail.com>
> > Sent: Friday, October 29, 2021 7:19 AM
> > To: amber.ambermd.org <amber.ambermd.org>
> > Subject: [AMBER] Constant pH MD simulation
> >
> > Hello everyone,
> >
> > I have been trying to carry out a constant pH MD simulation using AMBER
> 18
> > with the help of the "Amber Advanced tutorial 18" for the first time.
> > However, for my system I now need to titrate CYS, LYS and TYR residues
> and
> > for which I need to know the titrable residue name of each which is not
> > mentioned in the tutorial.
> > I'd really appreciate it if anyone could help me out with this.
> >
> >
> > *Regards,*
> >
> > *Divya Rai*
> >
> > *Research Scholar*
> >
> > *Department of ChemistryIndian Institute of Technology, Kharagpur*
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > ------------------------------
> >
> > Subject: Digest Footer
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > ------------------------------
> >
> > End of AMBER Digest, Vol 3526, Issue 1
> > **************************************
> >
> --
> *Regards,*
>
> *Divya Rai*
>
> *Research Scholar*
>
> *Department of ChemistryIndian Institute of Technology, Kharagpur*
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Nov 01 2021 - 07:30:03 PDT
