The manual describes how it's done using the cpinutil.pl script. Look at
chapter 4.9 (p. 133) of the Amber11 manual.
Good luck,
Jason
On Tue, Feb 22, 2011 at 11:50 PM, Cheng-I Lee <biocil.ccu.edu.tw> wrote:
> Dear Adrian,
>
> I've followed the manual of AMBER 11 for constant pH calculations, but I
> don't understand how to write the cpin file.
> Could anyone help me with cpin?
>
> The studied protein is a miniprotein with 23 amino acids:
> NTYR ARG VAL PRO SER TYR AS4 PHE SER ARG SER AS4 GL4 LEU ALA LYS LEU LEU
> ARG
> GLN HIP ALA CGLY
> prmtop file (bba.top) is attached.
>
> Thanks a lot!
> Sophia
>
> On Wed, Feb 16, 2011 at 10:27 PM, Adrian Roitberg <roitberg.qtp.ufl.edu
> >wrote:
>
> > Dear Sophia.
> >
> > It looks to me that before trying to to replica exchange and pH changes,
> > you should familiarize yourself with just the regular constant pH runs.
> >
> > Try looking at the manual and/or the constant pH files under the tests
> > directory in the amber directory.
> >
> > Adrian
> >
> >
> > On 2/16/11 12:55 PM, Cheng-I Lee wrote:
> > > Dear Adrian and Jason,
> > >
> > > Thanks for the reply.
> > > What's difference between temperature space and pH-space? Could you
> > please
> > > provide me some references?
> > >
> > > I'm interested in simulation of protein dynamics under specific pH
> > values. I
> > > have AMBER 11 to work on and hope to work on it asap.
> > >
> > > Sophia
> > >
> > > On Tue, Feb 15, 2011 at 9:34 PM, Adrian Roitberg<roitberg.qtp.ufl.edu
> > >wrote:
> > >
> > >> Hi Sophia
> > >>
> > >> If you want your replicas in temperature space, we can try to help
> you.
> > >> If you want your replicas to span pH-space, we just finished
> > >> implementing it in amber, but the code it still being debugged. Almost
> > >> surely we will release it for Amber 12.
> > >>
> > >> Best Regards
> > >> Adrian
> > >>
> > >>
> > >> On 2/15/11 2:30 PM, Cheng-I Lee wrote:
> > >>> Dear Amber users,
> > >>>
> > >>> I'm looking for a tutorial to run REMD at constant pH. Does anyone
> know
> > >> any
> > >>> website that shows REMD simulation at constant pH?
> > >>>
> > >>> Thanks a lot!
> > >>>
> > >>> Best wishes,
> > >>> Sophia
> > >>> _______________________________________________
> > >>> AMBER mailing list
> > >>> AMBER.ambermd.org
> > >>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>
> > >>
> > >> --
> > >> Dr. Adrian E. Roitberg
> > >> Associate Professor
> > >> Quantum Theory Project, Department of Chemistry
> > >> University of Florida
> > >>
> > >> on Sabbatical in Barcelona until August 2011.
> > >> Email roitberg.ufl.edu
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >>
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> > --
> > Dr. Adrian E. Roitberg
> > Associate Professor
> > Quantum Theory Project, Department of Chemistry
> > University of Florida
> >
> > on Sabbatical in Barcelona until August 2011.
> > Email roitberg.ufl.edu
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> 李政怡
> Cheng-I (Sophia) Lee
> Assistant Professor
>
> Department of Life Science
> National Chung Cheng University
>
> Phone: 1-886-5-2720411 # 66511
> Fax: 1-886-5-2722871
> E-mail: biocil.ccu.edu.tw
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Feb 23 2011 - 06:00:07 PST
