Hello Soumendranath,
I just worked on same thing and didn't get what I was expecting after reading all the papers recommending MMGBSA method over other scoring methods. I wished to rescore docking poses after minimization BUT to my surprise I got energy values more than 1000 Kcal/mol which I found amusing. Moreover, there was no trend in the values. Hence, I moved to rescore with docking software
Do let me know if you have some tips to improve the results
Best,
Nitin
-----Original Message-----
From: Soumendranath Bhakat [mailto:bhakatsoumendranath.gmail.com]
Sent: Monday, May 19, 2014 3:30 AM
To: AMBER Mailing List
Subject: [AMBER] QM/MM based binding free energy analysis AMBER
Dear Amberists;
It has been noticed that recent developments in QM/MM based parametirization raised some better approximation of binding free energy close to experimental counterpart. For literature:
http://www.ncbi.nlm.nih.gov/pubmed/22210962
Literature and some other trails suggested that DFTB-SCC level QM/MM approximation might leads to a better approximation than MM one.
I am just qurious if AMBER developers tried some test runs to check the effect of QM/MM based free energy calculations compared to experimental one for a better approximation of binding free energy?
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Sun May 18 2014 - 13:00:03 PDT
