Hi,
Another possibility is to use the GridMAT-MD tool:
http://www.bevanlab.biochem.vt.edu/GridMAT-MD/
The program needs only a xxx.gro file, which can be produce by using vmd.
HTH,
Balazs
Idézet (Benjamin D Madej <bmadej.ucsd.edu>):
> Given that your transmembrane protein is cylindrical, it should be
> possible to subtract the protein area from the total area.
>
> It really depends on how precise this needs to be modeled. A naive
> calculation of a circular area based on the radius of the protein
> could be done. On the other end of the spectrum, the area could be
> calculated using a convex hull algorithm and area calculation, using
> the X and Y coordinates of the protein that has been aligned with
> the Z axis, taking into account the van der Waals radius. As long as
> the area is consistent throughout the bilayer, it should be possible.
>
> Offhand, I don't know of any program that will do this currently.
> Perhaps others on the mailing list know of a program or script to do
> this? I think this will take some clever scripting with ptraj or
> another program to go through the trajectory file.
>
> Ben Madej
> Walker Molecular Dynamics Lab
> ________________________________________
> From: Fabrício Bracht [bracht.iq.ufrj.br]
> Sent: Wednesday, August 22, 2012 3:39 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] area per lipid popc membrane
>
> 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 - 22:30:04 PDT
