Hello Ben. Thank you for your suggestions. Indeed, I expect the volume
per lipid (and also the area per lipid) to change by the influence of
the protein on it. Actually, someone had suggested that I analyzed
lipids that are nearby the protein and the lipids that are not
directly interacting with the protein to see if there is any change.
Since you mentioned about the protein size, I have one other
simulation in which the protein is indeed a simple cylindrical
transmembrane protein. Would you happen to have any suggestions on
that particular case?
Thank you
Fabrício
2012/8/22 Benjamin D Madej <bmadej.ucsd.edu>:
> 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 - 16:00:03 PDT
