calculate the electrostatic potential of your protein and see if the
hydrophobic part of the ligand is exposed to the hydrophobic part of the
protein, the aromatic residues have partial negative charge and its also
hydrophobic.
On Thu, Feb 16, 2017 at 2:08 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
>
>
> Sent using OWA for iPhone
> ________________________________
> From: Thakur, Abhishek <axt651.miami.edu>
> Sent: Wednesday, February 15, 2017 4:40:14 AM
> To: amber.ambermd.org
> Subject: [AMBER] Hydrophobic and pi-pi interaction
>
> Hi everyone,
>
> I want yo know is there any way by which I can calculate hydrophobic
> interaction of my ligand.
>
> I could easily do hydrogen bond analysis, similarly it would be great if
> there is a way to calculate such calculations.
>
> It will be great if I can calculate some pi-pi interactions.
>
>
>
> With regards,
>
> -AT
>
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Received on Thu Feb 16 2017 - 08:30:02 PST
