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/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
===================================================================
xhu1.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.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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Received on Tue Sep 28 2004 - 21:53:00 PDT
