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 Post subject: Handling charged ligands
PostPosted: Mon Mar 14, 2016 1:24 am 
Millimolar User
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Joined: Tue Mar 03, 2015 1:46 am
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I am working on docking of some charged ligands to an active site. The site contains a metal ion (to which I assigned a positive charge). I noticed that ADT does not handle correctly the charge (eg for a deprotonated oxygen, coming in sdf format, it gives a partial charge far away from -1), I guess this is due to the fact that does not get the bond information of an sdf. So far, I managed by getting a mol2 file from my sdf in babel, with the already calculated Gasteiger charges and preserve these charges during the preparation step. The preliminary results from Autodock I got are kind of plausible, though I have to experiment more. Now, I am trying to do the same with vina, but it ignores the charges contained in the pdbqt and therefore again I guess it does not recognize the deprotonated oxygen and the results are different. Is there any way to assign these charges, or to deal with charged ligands? Thanks in advance

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