[AMBER] 回复: Query regarding pi-pi stacking interaction

From: 郭 家藩 via AMBER <amber.ambermd.org>
Date: Thu, 2 Nov 2023 07:10:06 +0000

Hi,
I think it should be very easy to implement that in cpptraj, please refer to this tutorial in AMBER-Hub. Measure the stacking percentage of a protein-ligand complex – AMBER-hub (utah.edu)<https://amberhub.chpc.utah.edu/stacking-percentage-protein-ligand-complex/>
And if you want to analysis other interactions, it maybe not very easy to preform in cpptraj. I think GitHub - cbouy/ProLIF: Protein-Ligand Interaction Fingerprints<https://github.com/cbouy/ProLIF> is a good alternative.


发件人: Sourav Bhowmik via AMBER<mailto:amber.ambermd.org>
发送时间: 2023年11月1日 15:42
收件人: amber.ambermd.org<mailto:amber.ambermd.org>
主题: [AMBER] Query regarding pi-pi stacking interaction

Dear users,

I have built up a system of 60 amino acid molecules of the same type. After
the simulation, I want to determine the pi-pi stacking interaction among
them. Could you please help me to calculate the same?

Regards,
Sourav Bhowmik
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Received on Thu Nov 02 2023 - 00:30:02 PDT
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