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PostPosted: Fri Sep 14, 2012 7:08 pm 
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Dear friends....

Recently i did DNA docking with a series of ligands. Everything was fine and the results were in good agreement with the experimental results. But unfortunately, when i started docking with a chloro substituted ligands, the output result has very high amount of energy, which is practically meaningless.

One thing more which i have found unique is that the Autodock 4.0 do not process the file which contain a name like "4-Cl". This was very strange !!!!!!

So i need your suggestions in this case..

Thanking You


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PostPosted: Fri Sep 21, 2012 3:42 pm 
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I have been some docking using chlorinated compounds with Vina. I haven´t observe any problems with them. Of course, my target has been protein not DNA. Have you tried using Vina instead of Autodock?


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PostPosted: Sat Sep 22, 2012 4:22 am 
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i havent tried Vina,

But the problem is that what may be the possible reason for such problem??? I mean, other result are good but only halegenated compounds are creating problem.

So do you have any idea ?


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PostPosted: Tue Oct 09, 2012 7:33 am 
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Ashan wrote:
i havent tried Vina,

But the problem is that what may be the possible reason for such problem??? I mean, other result are good but only halegenated compounds are creating problem.

So do you have any idea ?



No Idea. but try Vina


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