[gmx-users] make_hole vs. genconf

Arneh Babakhani ababakha at mccammon.ucsd.edu
Tue Sep 19 09:26:48 CEST 2006

Dear GMX Users,

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?)

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?

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 



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