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
>
>
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>
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> ------------------------------
>
> End of AMBER Digest, Vol 3526, Issue 1
> **************************************
>
--
*Regards,*
*Divya Rai*
*Research Scholar*
*Department of ChemistryIndian Institute of Technology, Kharagpur*
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Received on Sat Oct 30 2021 - 12:30:02 PDT
