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PostPosted: Thu Aug 13, 2009 5:54 pm 
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Hi,

I am pretty new to AUTODOCK. I tried to dock my ligand on a macro-molecule which contains potassium ion. Now the parameter file doesn't contain the parameters for K+. I tried to get these values and add them, but I didn't find them.
I have just been able to find Rij_hb and Rii. I am having problem with solvation radius and well depth and few other parameters. Can anybody give me these values or advise me as to how to approach this problem.

Thanks.


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PostPosted: Sat Aug 15, 2009 8:38 am 
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Do you have some reason to believe that this potassium ion is biologically relevant?

If you look in the autodock src directory, there should be a file named AD4_PARM99.dat, which , I believe, has Amber99-based parameters for potassium. You might try this as a starting point.


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PostPosted: Thu Aug 20, 2009 3:17 am 
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Thanks a ton. Yes, the potassium atoms are relevant in the pdb file I am working with. The program seems to be working fine now. :D


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