Re: [AMBER] Calculating area per lipid for system with different numbers of lipids on leaflets

From: Daniel Roe <>
Date: Tue, 23 Jul 2019 12:15:52 -0400


The only way to do something like this currently with cpptraj is to do
two separate 'areapermol' commands for each leaflet E.g.

areapermol Top <top leaflet mask> out apm.dat
areapermol Bot <bottom leaflet mask> out apm.dat

As Prajwal mentioned, this is only a very rough estimate of the actual
area per lipid. It would be nice if the area per molecule method in
cpptraj were improved a bit (code contributions to the GitHub
repository are encouraged and highly appreciated!).

Hope this helps,


On Tue, Jul 23, 2019 at 5:24 AM Maria Bzówka <> wrote:
> Hi All,
> I want to ask how (or if) I should change the method for calculating area
> per lipid for a POPC membrane with the transmembrane helix when the number
> of lipids on the leaflets differs (on the upper leaflet I have 65 lipids,
> while on the lower leaflet I have 66 lipids).
> Normally, I calculate it with: Area per lipid = (box X dimension)*(box Y
> dimension)/ number of lipids per layer (steps described in the Amber
> Lipid14 tutorial).
> Thank you in advance
> Maria
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Received on Tue Jul 23 2019 - 09:30:02 PDT
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