I'd like to build some lipids around a peptide. Can I do so using
genconf? (I know genconf can be used to build a membrane. I'm
asking if genconf can be used to build a membrane around a solute,
like a transmembrane protein?)
"around"? No.
I'm also aware of the make_hole tool. My question here is: Does
make_hole create a hole of specified dimensions and orientation,
according to the solute coordinates? And can you specify exactly
where in the membrane you want the whole?
Make_hole doesn't actually make a hole. You need to make the
premilinary hole yourself. The general problem is that if you take out
all lipids that contact the protein, then you will have a huge vaccuum
aroung the protein. So first you take out all the lipids whose
headgroup clashed (manually) then run make_hole to bend the tails out
of the space that is to be occupied by the protein, then add the
protien.
You will need to install gromacs-3.1.4 to do this.
So basically what I'm asking is: If you want to make a starting
structure (or several structures) with the solute (a peptide) in a
specific part of the membrane, is it better to set the desired
coordinates of the peptide first and then build a membrane around
it? Or, is it wiser to start with an equilibrated membrane and use
make_hole to create your hole first at the desired coordinates, then
insert the peptide?
1. Build your membrane (or find coords somewhere)
2. equilibrate it
3. Use make_hole or inflategro (I have never tried this one)
http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis
4. re-equilibrate
Reason not to do it all at once is because you want to limit your
protein's exposure to vaccuum, although I suppose you could use
position restraints to solve this issue (heavy atom on the protein and
a z-only on the lipid phosphate).
Chris
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