Re: [AMBER] Magnesium ion and MMPBSA/GBSA

From: Elvis Martis <>
Date: Mon, 12 Dec 2016 13:25:59 +0530

I am not sure how good this suggestion will be, perhaps someone will give
you a better suggestion.
But can try this,
While extracting frames for GB/PB calculations using atom number in, include the atom number of Mg in the receptor.


*Elvis Martis* Ph.D. Student, Bombay College of Pharmacy
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On 12 December 2016 at 13:14, Francesco Gentile <>

> Hello,
> I am running free energy calculations on a series of protein-ligand
> complexes. The ligands are all interacting with a magnesium ion in the
> active site of the enzyme. How should I treat the magnesium ion (part of
> the receptor, the ligand or what else?)? Also, does someone has experience
> with this kind of situation and maybe can help me in setting up correctly
> the calculation? Thanks in advance
> --
> Francesco Gentile
> PhD Student, Biophysics
> CCIS 3-215, Department of Physics
> 7-112, Li Ka Shing Centre for Health Research Innovation
> University of Alberta, Edmonton, AB T6G 2E1
> Canada
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Received on Mon Dec 12 2016 - 00:00:03 PST
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