[AMBER] mm-gbsa with more than one receptor

From: Liao <liaojunzhuo.aliyun.com>
Date: Thu, 12 Dec 2019 19:39:01 -0600

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
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Received on Thu Dec 12 2019 - 18:00:03 PST
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