[gmx-users] Angular probability function

[João Henriques]

Quick note, I didn't type the actual "X" in the selection, X can be any
protein atom I want to select, like O or CA, etc.

/J

On Tue, Oct 4, 2016 at 3:21 PM, João Henriques <
joao.henriques.32353 at gmail.com> wrote:

> 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
>
>