ADL: Urgent for my Ph.D. thesis and my career

L. Michel Espinoza-Fonseca mef at ddt.biochem.umn.edu
Fri Apr 10 03:01:16 PDT 2009


Mostafa,

I agree with Mark: you definitively need to share your dlg file with
us so we can help you better. 'm pretty sure your problem has nothing
to do with the algorithm, but with an incorrect setting-up of your
protein or your ligand, which is producing an extremely favorable
electrostatic interaction. You should take a look at the contribution
of each term to the free energy of binding, this will give you a
better hint on what's going on.

Cheers,
Michel

On Fri, Apr 10, 2009 at 11:39 AM, Gavin Seddon <home at gavsed.net> wrote:
> mswingle at jaguar1.usouthal.edu wrote:
>>
>> Mostafa,
>> It would be helpful if you could post more information from the dlg file.
>> For example, what are the values of the different free energy components
>> (electrostatic, internal energy etc.)? Do the structures of the docked
>> complexes of these conformers look reasonable?
>> Regards,
>>
>> Mark
>>
>> ----- Original Message -----
>> From: Mostafa El-Miligy <melmiligy4m at yahoo.com>
>> Date: Thursday, April 9, 2009 3:09 pm
>> Subject: ADL: Urgent for my Ph.D. thesis and my career
>> To: autodock at scripps.edu
>>
>>
>>
>>>
>>> Hi
>>>  I used Autodock-4 for blind docking inside Trypanosoma Cruzi
>>> Trypanothione Reductase (PDB 1AOG) and Telomerase reverse transcriptase (PDB
>>> 3DU6) enzymes and some of the docked compounds showed estimated free energy
>>> of binding more than -70000000 Kcal/mole for the first 4 ranked conformers
>>> so is it a logic or acceptable calculation or not ? and if it is acceptable
>>> what is the explanation of this very low energy ?. However, the 5th
>>> conformer showed binding energy in a normal range around -5 to -10
>>> Kcal/mole.
>>> Please reply to me as soon as possible because my Ph.D. supervisor Dr Aly
>>> Hazzaa said that Autodock-4 is a bad software and not working good. so
>>> please reply to me on this problem because it will affect my career badly.
>>>  Thank you
>>>  Yours,
>>> Mostafa El-Miligy
>>>
>>> Mostafa El-Miligy
>>>
>>> Ph.D. student Department of Pharmaceutical Chemistry
>>> Faculty of Pharmacy
>>> University of Alexandria
>>> Egypt
>>>
>>>
>>>
>>>      ________________________________________________
>>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>>>
>>
>> ________________________________________________
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>>
>>
>
> Ok, these issues keep popping up on the list and I/WE are looking into
> reasons, it may be the ad4 algorithm and I would like to see it.  In the
> meantime one could argue -7x10e7 kj/mol would be
> -7e7 / e23
> ~-7e-16kj/molecule
> does this sound better? Or, if your supervisor keeps moaning tell him to
> stop and BUY GOLD from the guys in Cambridge but, this is still a genetic
> algorithm software!  And I think it doesn't use Lamarkian like AD4 does!
>
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