AMBER Archive (2004)

Subject: Re: AMBER: question about delphi and UHBD

From: xhu1_at_memphis.edu
Date: Tue Sep 28 2004 - 17:06:12 CDT

Yes. it's correct. Thank you Carlos.

Shawn

----- Original Message -----
From: Carlos Simmerling <carlos_at_ilion.bio.sunysb.edu>
Date: Tuesday, September 28, 2004 2:46 pm
Subject: Re: AMBER: question about delphi and UHBD

> did Delphi correctly read your charges? look at the output file
> to make sure.
>
> ===================================================================
> 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_at_stonybrook.edu
> ===================================================================
>
>
>
>
> xhu1_at_memphis.edu wrote:
>
> >Dear Dr. Thomas Cheatham,
> >
> >Thank you very much for your reply. I didn't mention the
> coulombic
> >energy difference(complex - receptor - ligand) in my previous
> email,
> >which is -302 kcal/mol in both programs. The final binding energy
> is
> >-37 kcal/mol in UHBD and 565 kcal/mol in delphi. The conversion
from
> >kt/e to kcal/mol is correct and both are running with the same
> >internal/exterior dielectric. But it is a good suggestion to run
> a
> >really simple test case. I gonna try. Thanks again.
> >
> >best
> >
> >Shawn
> >
> >----- Original Message -----
> >From: "Thomas E. Cheatham, III" <cheatham_at_chpc.utah.edu>
> >Date: Tuesday, September 28, 2004 1:34 pm
> >Subject: Re: AMBER: question about delphi and UHBD
> >
> >
> >
> >>Dr. Luo wrote:
> >>
> >>
> >>
> >>>Aside from different numerical implementations of molecular
> >>>
> >>>
> >>surface and
> >>
> >>
> >>>finite difference solvers, Delphi and UHBD also use very different
> >>>methods to compute reaction field energies. So in the end, you
> >>>
> >>>
> >>can't get
> >>
> >>
> >>>agreement at all for a complex molecule, such as a large protein.
> >>>
> >>>
> >>From the original e-mail of Shawn:
> >>
> >>
> >>
> >>>The final solvation energies for ligand, receptor and complex are
> >>>-1466, -1529 and -2730 kcal/mol in UHBD and -1035, -1056, -1224
> >>>kcal/mol in delphi.
> >>>
> >>>
> >>Despite the different algorithms used and the size of the
> systems
> >>beingstudied, I find it rather difficult to believe that these
> >>differences in
> >>energetics are reasonable between the two programs. One program
> >>suggestsa free energy difference of 265 kcal/mol and the other
> 867
> >>kcal/mol for
> >>the complex - (receptor + ligand) favoring the separated
> proteins.
> >>Both
> >>of these are completely unreasonable (if they are the final
> solvation>>energies). The disagreement between the two methods
> makes me
> >>wonder if
> >>the numbers are indeed comparable. Do the continuum solvation
> >>
> >>
> >numbers
> >
> >
> >>include anything else that you do not realize? Is the
> conversion
> >>
> >>
> >from
> >
> >
> >>reaction field energy to kcal/mol correct? Are both running
> with
> >>the same
> >>internal dielectric? Even generalized Born and continuum
> methods, in
> >>general, show better agreement than is seen between UHBD and
> >>delphi shown
> >>above leading me to speculate that something is amiss either in the
> >>running or interpretation of the results. I do not think this
> >>relates too
> >>heavily to the number of iterations.
> >>
> >>To test out your knowledge of delphi and UHBD, try running a
> >>really simple
> >>test case, like a continuum run on an isolated Na+; both
> programs
> >>shouldgive a number around 97 or so for the Na+ parameters
> (Aqvist
> >>adapted)present in AMBER.
> >>
> >>Good luck.
> >>
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> >>
> >>
> >
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