I have one more doubt regarding this.
Now, I am using a basic solvent pH(~8). For my system, there are 2 CYS
residues involved in a disulphide linkage (and thereby are present in the
pdb with the resname "CYX"). So, do I need to change the resnames
accordingly (i.e. "CYS") so as to be able to titrate them or should I keep
them as it is (i.e. "CYX").
*Regards,*
*Divya Rai*
*Research Scholar*
*Department of ChemistryIndian Institute of Technology, Kharagpur*
On Mon, 1 Nov 2021 at 19:39, Jason Swails <jason.swails.gmail.com> wrote:
> 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
>
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Received on Wed Nov 10 2021 - 05:00:02 PST
