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Docking/Neutralization how and in which order?
#36210 02/02/17 12:43 AM
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mretier Offline OP
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Hi all,
I just started playing around with CHARMM.

I have a protein structure that I can minimize in vacuum.
I know the structure binds three Mg-ions.
Eventually, I want to fit those ions and two ligands to that structure.

Following the tutorials, it is not clear to me what my next steps should be. The way I understand it is that I would first have to 'neutralize' the protein to add the desired ions, but how do I progress from there?

Can someone point me in the correct direction?

Best,
Michael

Re: Docking/Neutralization how and in which order?
mretier #36214 02/02/17 10:39 PM
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rmv Online Content
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Insufficient data to formulate a response.

A lot depends on the intended purpose of the model under construction, along with the origin of the protein (and any other) coordinates.

CHARMM is fairly complex research tool, and is best learned in a research group with other active users of the program. Self-study with the somewhat limited (and dated) web tutorials may be a tough way to go.



Last edited by rmv; 02/03/17 12:57 AM. Reason: more text

Rick Venable
computational chemist


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