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
peptide?
Thanks,
Arneh
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