[gmx-users] make_hole vs. genconf

Arneh Babakhani 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)
> 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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