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

Gavin Seddon home at gavsed.net
Fri Apr 10 02:39:38 PDT 2009


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 ---
>>     
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
>   
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!



More information about the autodock mailing list