[AMBER] absolute binding free energy calculations

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Fri, 22 Nov 2019 18:37:22 +0000

Dear Amber users,

I have been trying to setup the binding free energy calculation of a protein + ethanol (small molecule weak binder), and I am struggling through the steps.

Would it be impossible to setup a tutorial in amber for TI based absolute free energy calculation, that would immensely help the community.

Besides the point, I have a few doubts.
I downloaded requisite input files from a recent publication by the Simmerling lab, and I realized they have the setup as this -----> Three folders named : 001.setup 002.eq 003.prod. Now the restrain weight is varied across the equilibration phase.
They have 1 input file for minimization, 1 input file for the heating, and the equilibration is broken down in 4 stepsÖ
The heating has a restraint_weight =100.00, equil1 restraint_weight is 10 and finally in production there is no restraint applied. Is this a general procedure?
In my case itís a weak binder and I need to keep restrains on it all times, will that affect my calculations?
Also, what is the way to analyse the results after running TI?

DO I care only about my production runs or will I have to analyze my equilibration steps too?




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Received on Fri Nov 22 2019 - 11:00:03 PST
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