# [AMBER] area per lipid popc membrane

From: Fabrício Bracht <bracht.iq.ufrj.br>
Date: Tue, 21 Aug 2012 18:25:28 -0300

Hello. I would like to know how can I calculate the area per lipid of
a popc membrane that has a peptide in it. I have already calculated
the area per lipid of the membane, but I do not know how to calculate
the area that the pepide occupies so that I can subtract from the area
of the membrane.
My ptraj script:
trajin mdcrd.npt_rest1
vector POPC :67-546 box out popc.vector

This gives me the file with:
# FORMAT: frame vx vy vz cx cy cz cx+vx cy+vy cz+vz
# FORMAT where v? is vector, c? is center of mass...
1 101.5922 98.0267 76.6249 0.0000 0.0000 0.0000 101.5922
98.0267 76.6249
2 101.3926 97.8341 76.3787 0.0000 0.0000 0.0000 101.3926
97.8341 76.3787
3 101.1971 97.6454 76.1716 0.0000 0.0000 0.0000 101.1971
97.6454 76.1716
4 101.0322 97.4863 75.9736 0.0000 0.0000 0.0000 101.0322
97.4863 75.9736
5 100.8363 97.2973 75.8005 0.0000 0.0000 0.0000 100.8363
97.2973 75.8005
6 100.6243 97.0927 75.6123 0.0000 0.0000 0.0000 100.6243
97.0927 75.6123
7 100.3761 96.8532 75.3892 0.0000 0.0000 0.0000 100.3761
96.8532 75.3892
8 100.2033 96.6865 75.1642 0.0000 0.0000 0.0000 100.2033
96.6865 75.1642
9 100.0209 96.5105 74.9660 0.0000 0.0000 0.0000 100.0209
96.5105 74.9660
.
.
.

By multiplying x and y and dividing by 80 I get the area per lipid of
the entire membrane without considering the area occupied by the
protein, right? Is there any way to calculate the cross section area
of the protein?
Thank you
Fabrício Bracht

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Received on Tue Aug 21 2012 - 14:30:05 PDT
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