[gmx-users] Angular probability function

[João Henriques]

Dear Users and Experts,

I need to calculate the angular distribution function formed by the water
O-H bond (OW-HW1 and OW-HW2) and a given atom of a protein (X). I assume
gmx gangle is the way to go, but I am not being able to get it to do what I
need.

*Quick note:* I first used trjorder to reorder the water molecules by
distance to the protein atoms, and then I defined the minimum number of
water molecules that constitute my "solvation layer" (based on the minimum
number of waters that always lay within a certain cutoff). Thus, my index
file only contains, say, the first 400 water molecules of a given frame of
the "reordered" trajectory.

Why doesn't this command achieve what I want?

gmx gangle -f xxx.xtc -s xxx.tpr -n xxx.ndx -oav avg.xvg -oh hist.xvg -binw
0.1 -g1 angle -group1 'atomname X OW HW*'

The wild card fails immediately, and even if I get rid of it and use X=O,
like so 'atomname O OW HW1' it also fails, saying that the number of atoms
is not divisible by 3... Plus, the index file being there or not, it
doesn't seem to matter, as all waters are used and not just the 400 I
defined.

I'm not new to gromacs in general, but I am a complete noob in terms of
versions 5.0 and above, and this selection syntax is killing me :) Any
input would be greatly appreciated.

Thank you in advance,
Best regards,
João