[gmx-users] princ and rotate

[K.A. Feenstra]

Chris Shaw wrote:
> 
> Hi all ,
> 
> I am trying in vain to use rotate and princ to align my helices
> along the x, y, z axes. I am also doing a similar operation
> with a lipid bilayer so that the bundle of helices is in the
> right orientation with respect to the bilayer. Could anyone who
> has used these please help and if poss point me in the right
> direction with regards to command line options.

editconf -princ -f in -o out

will orient your helix in file in.gro with its long axis along x,
and shortest axis along z. However, what you consider long and short
might differ slightly from editconf's opinion: large extended side
chains (e.g. lysine, arginine) might give significant differences.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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