Re: [AMBER] REMD at constant pH

From: Cheng-I Lee <biocil.ccu.edu.tw>
Date: Wed, 23 Feb 2011 12:50:39 +0800

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



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Received on Tue Feb 22 2011 - 21:00:02 PST
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