[AMBER] peptide-bilayer MD simulation analysis

From: golshan bakrani <golshan7193.gmail.com>
Date: Mon, 18 Feb 2019 09:20:35 +0330

Dear Amber community,

I performed MD simulation on a peptide in interaction with bilayer membrane
(peripheral peptide) to see the effect of the peptide on the membrane. I
want to check the membrane parameters with cpptraj but I cannot find proper
scripts in the manual for my analysis such as:

- Protein-membrane interaction analysis

- Volume per lipid

- Lateral diffusion of lipids

- Membrane curvature during of protein interaction

- Membrane thickness and its changes during simulation

I would appreciate if somebody could help me in this issue.

Best regards.

 P.S. similar analyses have been done in the following article but they did
not mention about the scripts they used.

Skjevik ÅA, Madej BD, Dickson CJ, Teigen K, Walker RC, Gould IR. All-atom
lipid bilayer self-assembly with the AMBER and CHARMM lipid force fields.
Chem Commun (Camb). 2015;51(21):4402-5.
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Received on Sun Feb 17 2019 - 22:00:02 PST
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