Thank you very much, Asim!!! it's a great help! Best ---Shawn
----- Original Message -----
From: Asim Okur <aokur.ic.sunysb.edu>
Date: Monday, April 4, 2005 12:36 pm
Subject: Re: AMBER: force constant Unit used in TMD
> Hi,
>
> I believe the 1st paper mentioned using Targeted MD in AMBER is
> the
> following one,
>
> Okur A, Strockbine B, Hornak V, Simmerling C
> Using PC clusters to evaluate the transferability of molecular
> mechanics
> force fields for proteins
> JOURNAL OF COMPUTATIONAL CHEMISTRY 24 (1): 21-31 JAN 15 2003
>
> Cheers,
>
> Asim
> Viktor Hornak wrote:
>
> >
> > If you need a paper that describes TMD method implemented in
> AMBER7
> > (and 8), here is the original reference (it's slightly different
> from
> > original TMD method proposed by Schlitter):
> >
> > Apostolakis J., Ferrara P, Caflisch A: Calculation of
> conformational
> > transitions and barriers in solvated systems: Application to the
> > alanine dipeptide in water.
> > J. Chem. Phys. 110(4), p. 2099 (1999)
> >
> > If you're looking for papers that used AMBER implementation of
> TMD,
> > I've seen a few but don't have specific references handy...
> >
> > Cheers,
> > -Viktor
> >
> > xhu1.memphis.edu wrote:
> >
> >> Thank you very much, Dr. Simmerling! Have you any suggestion
> about
> >> reference of TMD using in AMBER? I can't find it in the manual.
> >> ThankS again.
> >> Regards
> >>
> >> Shawn
> >>
> >> ----- Original Message -----
> >> From: Carlos Simmerling <carlos.ilion.bio.sunysb.edu>
> >> Date: Monday, April 4, 2005 11:06 am
> >> Subject: Re: AMBER: force constant Unit used in TMD
> >>
> >>
> >>> the energies reported by Amber are in units of per mole.
> >>> Nothing is per molecule. This goes for the force constants as
> well.>>>
> >>>
>
===================================================================>>>
Carlos L. Simmerling, Ph.D.
> >>> Associate Professor Phone: (631) 632-1336
> >>> Center for Structural Biology Fax: (631) 632-1555
> >>> Stony Brook University Web:
> >>> http://comp.chem.sunysb.edu/carlosStony Brook, NY 11794-5115
> E-
> >>> mail: carlos.simmerling.stonybrook.edu
> >>>
>
===================================================================>>>
> >>>
> >>>
> >>>
> >>> xhu1.memphis.edu wrote:
> >>>
> >>>
> >>>> Dear Amber users,
> >>>>
> >>>> I have a question about Targeted MD: what's the unit of force
> >>>
> >>> constant
> >>>
> >>>> used in TMD, kcal/(molecule*A^2) or kcal/(mole*A^2)?
> according to
> >>>
> >>> the
> >>>
> >>>> energy term: E=0.5* TGTMDFRC * NATTGTRMS * (RMSD-TGTRMSD)**2,
> it
> >>>> should be kcal/(molecule*A^2). Am I right? Sorry for this
> simple
> >>>> question. Thank you very much!
> >>>>
> >>>> Best
> >>>>
> >>>> Shawn
> >>>>
> >>>> --------------------------------------------------------------
> ----
> >>>>
> >>> -----
> >>>
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majordomo.scripps.edu
> >>>>
> >>>>
> >>>>
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> >>>
> >>
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> >
> >
>
> --
> Asim Okur
> Stony Brook University
> Chemistry Department
> Stony Brook, NY 11794-3400
> 631 - 632 1560
>
>
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Received on Mon Apr 04 2005 - 19:53:01 PDT
