HI,
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
mm_pbsa.pl, include the atom number of Mg in the receptor.
Regards
*Elvis Martis* Ph.D. Student, Bombay College of Pharmacy
[image: photo] Email: elvis_bcp.elvismartis.in <elvis_bcp.elvismartis.in>
Website: http://www.elvismartis.in <http://www.elvismartis.in/>
group website: http://www.profeccoutinho.net.in/
Address:
Kalina, Santa Cruz [E]
, Mumbai, 400 098, INDIA
Alt. e-mail: emartis12.live.com
<
https://in.linkedin.com/in/elvisadrianmartis>
On 12 December 2016 at 13:14, Francesco Gentile <fgentile.ualberta.ca>
wrote:
> 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
