ADL: no inhibition constante (Ki)

Tee Pioj tee_piorj at yahoo.com
Wed Mar 5 00:36:16 PST 2008


Hi Miguel,
Because I encountered this problem before and tried the method I suggested you. Didn't it work? Talking to the term crash, you can noticed in your dlg file. I have to say that every time the binding energy is too high, there will be some of vdw value (after xyz coordinate) being +99.99. That' s an error. You try to check this comformation of inhibitor with macromolecule in 3D program. Then, you focus on active site region (show atom/molecule of active site as well) and see if there is any part (any atom) of inhibitor and macromolecule overlap or crash each other. If any, I think it may be cause the problem. Also, if you try to check comformation of reasonable binding energy, you won't see any of what I mentioned above.

Best luck,
Tee Piroj 


----- Original Message ----
From: Miguel Quiliano Meza <qilime at yahoo.es>
To: autodock at scripps.edu
Sent: Tuesday, March 4, 2008 10:25:23 PM
Subject: Re: ADL: no inhibition constante (Ki)

Hi Tee

Please.. can you give me the reasons.. why do you think this procedure works? Also I extracted file (conformations) where the ligand is very close with macromolecule (my ligand is an inhibitor).. maybe is reasonable.. can you explain me the term "crash" in this case?

Also.. I forgot.. but this problem is accompanied with the problem.. reported by Renuka Varanas....... >  ADL: Cannot load the conformations. (today in the list).

so.. If someone can help us.. I would be very grateful.

thanks in advance.

Atte
Miguel.

Tee Pioj <tee_piorj at yahoo.com> escribió: Hi ! Miguel
I see your problem. This happened because some components(atoms) of your ligand crashed with Macromolecule. You can extract file to display what happened using 3D program such as Weblab viewer. That why the binding energy was so far and Ki didn't appear. To solve this problem, try to redock by increasing number of run (about 30 to 50 runs but It's sure that more time is consumed). Then, see the result in your out.dlg to see which one has resonable value of dock energy ( not too much high or being positive).. After that, extract the comformation corresponded to the value using egrep command or get-docked( from autodock package) and redocking again. I guess this time will give you reasonable result.

Best luck,
Tee Piroj 


----- Original Message ----
From: Miguel Quiliano Meza 
To: autodock at scripps.edu
Sent: Tuesday, March 4, 2008 1:00:19 AM
Subject: ADL: no inhibition constante (Ki)

Hi dockers.

I have been performing several dockings as a training. But in some cases inhibition constant term is not coming (in the out.dlg). Also I have read a same question in the list but no-one responds.

Also in some cases my binding energy  is  16700000 ..!!!!

so I would like to know  in which cases the Ki will come? and why not?

Thanks in advance.

Miguel



      
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