Re: [AMBER] Comparison of the results

From: manikanthan bhavaraju <>
Date: Thu, 8 Mar 2012 16:19:50 -0600

Thanks for the comment. I am really sorry for the confusion. I should
have been more clear. Yes, I am talking about normal modes
calculations using

Yes, all the TI results are converged.

Now coming to the PBSA/GBSA calculations. I have performed 13ns of
equilibration and took last 5ns for PBSA/GBSA. I have merged the 5ns
mdcrd files as one, and used script to calculated PB/GBSA
over 250 snapshots. Similarly, nmode calculations were done for 10
snapshots. Is it better to perform the calculations individually
(1ns) ?

I have done literature review on nmode calculations for protein-ligand
system. In some of the papers, the binding affinities values were
lower than nmode values, resulting in a negative deltaG. So, I am not
sure how to resolve my problem.


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Received on Thu Mar 08 2012 - 14:30:05 PST
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