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

Sampo Karkola sampo.karkola at helsinki.fi
Thu Oct 11 14:40:40 CEST 2007

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

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 

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.

I'm using Gromacs 3.3.1 on an Ubuntu 7.04.

Any help is appreciated!


Sampo Karkola
Doctoral student

Laboratory of Organic Chemistry
Department of Chemistry
POBox 55, FIN-00014
University of Helsinki

tel. +358 9 191 50369
fax. +358 9 191 50366
sampo.karkola at helsinki.fi

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