[AMBER] What is the best way to study a dynamics route of a molecule to enter a protein

From: Wenyu Qian <qianwenyu01.gmail.com>
Date: Tue, 25 Aug 2015 16:04:08 -0600

Hello all,

I have a protein with an empty pocket. I want to calculate the free energy
of insertion of a molecule from solution to that pocket. I have a sort of
idea on the pathway it should take.

I think I can do this with umbrella sampling, but I am not sure how to. I
viewed the tutorial about umbrella sampling, but it was only about
conformational change.

Is there anything you recommend that is similar to what I want to do?

Best regards,
Wenyu "Mac" Qian
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Received on Tue Aug 25 2015 - 15:30:03 PDT
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