Hi think you can simply define both proteins as the receptor. Just define both of the proteins‘ residues as the receptor in generating its prmtop file.
Sent from my iPhone
> On Dec 12, 2019, at 5:50 PM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
>
> Hello AMBER List,
>
> I have simulated a system (single trajectory) with 3 proteins wherein the
> peptide is bound to 2 proteins. I am interested in calculating the free
> energy of binding using GBSA method. Is there a way to specify two proteins
> as receptors in the gbsa script or I have to perform the gbsa analysis
> twice considering each protein as a receptor?
>
> Many thanks,
> Neha
>
> --
> Regards,
> Dr. Neha S. Gandhi,
> Vice Chancellor's Research Fellow,
> Queensland University of Technology,
> 2 George Street, Brisbane, QLD 4000
> Australia
> LinkedIn
> Research Gate
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Dec 12 2019 - 18:00:02 PST
