[gmx-users] make_hole vs. genconf
ababakha at mccammon.ucsd.edu
Tue Sep 19 21:30:15 CEST 2006
Great, thanks Chris!
chris.neale at utoronto.ca wrote:
>> 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)
> 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).
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