ADL: Non-integral charges

Rocco Moretti roccomoretti at hotpop.com
Mon Jan 23 10:03:32 PST 2006


yingting liu wrote:
> Dear Sir/Madam,
> 
> I am trying to dock atp to a protein kinase. I used
> the non-hydrogen pdb file of ATP and added all of the
> hydrogens by ADT. However, each time, when I tried to
> load the fixed pdb file as a ligand, ADT warned me
> that the total charge error is 0.499. Could you please
> tell me how I can fix this problem? Will the 
> non-integral charges effect my docking results
> significantly?
> 
> Thank you very much!
> 
> Tina Liu 

I posted the same problem a short while back. The suggestion I got was 
to use the PRODRG server for charge assignment:

http://davapc1.bioch.dundee.ac.uk/programs/prodrg/

HTH


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