[gmx-users] non-existent angles found from trajectory g_angle

Mark Abraham Mark.Abraham at anu.edu.au
Thu Oct 11 15:51:07 CEST 2007

Sampo Karkola wrote:
> Dear list,
> I have a simulation trajectory of a CYP enzyme with a ligand in a 
> truncated octahedron box with water and ions. The simulation went nice 
> with stabilising backbone rmsd and potential and total energies. Now I'm 
> interested in an angle formed by two atoms in a ligand and the heme 
> iron. I tried to get the average angle as a function of time and the 
> angle distribution during the simulation using g_angle. The angle in 
> question is defined as a atom triplet in the index file. If I analyse 
> the trr file with
> g_angle -f file.trr -s file.tpr -n indexfile -ov aver -od distr
> I get a peak of angles around 120 deg (which it should be) and 
> additionally another peak around 50 deg. If I visualise the trajectory 
> with vmd after
> trjconv -f file.trr -s file.tpr -o new.gro

VMD can read a .trr file. Load a corresponding structure file and then 
import the trajectory into it, like in the VMD tutorials for NAMD (et 
al.) trajectories.

> I cannot see any of those angles around 50 deg. So how come g_angle 
> finds angles that are not there? I have checked that the atom triplet in 
> the index file is correct. I'm guessing that due to pbc the ligand jumps 
> out of the box and the angle is calculated between the iron in one box 
> and the two ligand atoms in another box and therefore producing weird 
> angles.
> Then I tried to remove pbc effects from the trajectory to 
> visualise/analyse the system properly and I performed (as suggested in 
> the list)
> trjconv -f file.trr -s file.tpr -o new.gro -center tric -pbc none(tried 
> also nojump and inbox) -ur compact
> and subsequently
> trjconv -f new.gro -s file.tpr -o new_fitted.gro -fit progressive
> After these procedures, the enzyme is nicely fitted and displayed as a 
> whole molecule but the ligand occasionally jumps out of the box and I 
> still get those weird angles.

Try making an index group that is the union of enzyme and ligand and 
then use trjconv -cluster.


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