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PostPosted: Mon Dec 20, 2010 1:36 pm 
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Could you any one help how to add charges for zinc metal in protein while docking?


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PostPosted: Thu Jan 20, 2011 10:18 pm 
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Hi Sangeetha,

you can manually change the charge in the PDBQT file to put the value that suits the best for your needs. One suggestion: avoid plan +2.0 charges, that are unrealistic and will boost too much the electrostatic maps.

Happy dockings,

Stefano


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PostPosted: Thu Aug 11, 2011 10:42 am 
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How would you change the charge in a pdbqt file exactly? using autodock(PMV)?


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PostPosted: Thu Aug 11, 2011 5:37 pm 
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Hi,

you should open the PDBQT file in a text editor (i.e. Gedit on Linux, Notepad on Windows...) and change manually the value of the charge in the file.

Code:
ATOM      1 Zn   XXX     1       3.698  -0.688  -0.036  1.00  0.00     0.000 Zn
becomes:
Code:
ATOM      1 Zn   XXX     1       3.698  -0.688  -0.036  1.00  0.00     1.500 Zn


Hope this helps,


Stefano


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PostPosted: Thu Nov 24, 2011 10:50 pm 
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Hi Stefano,

I am also using AD4.2 where zinc is my ligand. I have noticed that u suggest a charge of 1.5, is there a reason for this? I have found a paper that does support ur suggestion. Can this be generalised (to free zinc ions), how about calcium and magnesium ions, what would u recommend as charges?

Thank you very much for your help!!

Sara


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PostPosted: Wed Jan 25, 2012 12:28 am 
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Is there any way to automatically change all the charges in the PDBQT file with the same parameters? What program would be best for this if possible?


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