Hello Fabricio,
Interesting question that you bring up here. If you'd like to only calculate the area per lipid for the phospholipids, you'll need to subtract the area of the protein. The problem is, your peptide area will probably vary through the lipid bilayer unless it is a a simple cylindrical transmembrane protein.
I think a better way to go about this would be to use the volume per lipid for comparison. This value has been measured experimentally for some phospholipids. It should be possible to calculate the volume for both the protein and the phospholipid bilayer. As far as I know, volume calculations are not available in ptraj or cpptraj, but I think are available in VMD.
Also, the bilayer density would be useful to examine as well. Our group has used Hannes Loeffler's 'Handy Routines for ptraj' for that: http://www.stfc.ac.uk/cse/25249.aspx
I would suppose that the interactions between the phospholipids and the protein will influence the volume per lipid value, especially depending on the number of phospholipids in your bilayer.
Ben
________________________________________
From: Fabrício Bracht [bracht.iq.ufrj.br]
Sent: Tuesday, August 21, 2012 2:25 PM
To: AMBER Mailing List
Subject: [AMBER] area per lipid popc membrane
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 Wed Aug 22 2012 - 11:00:04 PDT
