Hello Soumendranath,
I went through few papers and followed the approach mentioned in J Comput Chem 32: 866-877, 2011 . I did minimization of the water and then of the selected residues + ligand in consecutive steps. Then I created .mdcrd file from minimized structure and calculated MMGBSA energy. However, as you results were scary.
Let me know your inputs on my approach and the paper I mentioned
Best,
Nitin
-----Original Message-----
From: Soumendranath Bhakat [mailto:bhakatsoumendranath.gmail.com]
Sent: Monday, May 19, 2014 3:48 AM
To: AMBER Mailing List
Subject: Re: [AMBER] QM/MM based binding free energy analysis AMBER
Hii Nitin;
Thats a bit of scary data 1000 kcal/mol. Though I am looking at some papers saying for QM/MM GBSA or PBSA such as
http://www.ncbi.nlm.nih.gov/pubmed/24490903 and
http://www.ncbi.nlm.nih.gov/pubmed/24631364
Did u perform a QM/MM based MD taking catalytic and crucial residues treated with QM parameter and then perform QM/MM GBSA or PBSA? Because 1000 kcal/mol is the most false approximation ever.
On Mon, May 19, 2014 at 1:08 AM, Nitin Sharma <sharmanitin.nus.edu.sg>wrote:
> 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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--
Thanks & Regards;
Soumendranath Bhakat
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Received on Sun May 18 2014 - 13:30:03 PDT
