Dear Maria,
Using the formula: Area per lipid (APL) = (box X dimension)*(box Y
dimension)/ number of lipids per layer, in case of protein-membrane system.
This formula overestimates the APL value.
You can try using this method to compute APL. It gives you precise answers
on APL for All lipids, Bound lipids, unbound lipids, etc.
Link:
https://github.com/prajwal07/Calculate_LIPID_parameters_using_Voronoi_Method
Thanks and best regards,
---------------------------------------------
Prajwal P. Nandekar, Ph.D. (Pharmacoinformatics)
Scientist, Schrodinger Inc. Bangalore
Mobile: +91-9872507189
Website: https://sites.google.com/view/prajwalnandekar
On Tue, Jul 23, 2019 at 2:54 PM Maria Bzówka <m.bzowka.tunnelinggroup.pl>
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 - 03:00:02 PDT
