[AMBER] MMGBSA question

From: George Tzotzos <gtzotzos.me.com>
Date: Mon, 16 Feb 2015 16:53:26 -0300

I’ve run a 100ns MD trajectory of a receptor liganded to two identical ligands.

My objective is to determine the relative binding energies of the ligands.

I’ve stripped the trajectory of water molecules, ions and ligand_1, prepared new topology files and performed MMGBSA.

I repeated the above process leaving in the complex ligand_1 and stripping ligand_2.

Is this approach legitimate?

Looking forward to your advice and comments

Regards

George



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Received on Mon Feb 16 2015 - 12:00:03 PST
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