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PostPosted: Thu Jan 23, 2014 10:33 pm 
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I am modeling a protein that contains an iron sulfur cluster. When I am building the grid I directly set the map types to include FE and S. However, when I choose the macromolecule and save the pdbqt I receive a message saying the atoms of the iron sulfur cluster have zero charge.

How can I add charges to the iron sulfur clusters? Below is a line from my PDB file describing an Fe atom.

HETATM 2771 FE SF4 A2460 44.551 0.719 23.738 1.00 14.24 Fe


Thanks!


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PostPosted: Wed Feb 12, 2014 6:00 pm 
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After you decide what charges you want to use, edit your pdbqt file(s) to add them.

For example, to add +2 charge to this ZN atom:
Change:
HETATM 2501 ZN ZN A 901 14.305 -14.100 -59.860 1.00 16.63 0.000 Zn
to:
HETATM 2501 ZN ZN A 901 14.305 -14.100 -59.860 1.00 16.63 2.000 Zn


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PostPosted: Fri Feb 14, 2014 3:35 pm 
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Wow, that was easy. Thank you so much!


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PostPosted: Fri Dec 26, 2014 8:28 pm 
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Thats easy not very hard
http://apkandroidsapp.blogspot.com


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