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

Sampo Karkola sampo.karkola at helsinki.fi
Fri Oct 12 09:57:25 CEST 2007

Hi Mark,

visualisation of the .trr file with vmd succeeded, but the original 
problem remains.The -pbc cluster option did not do any better. The weird 
thing is that after trjconv with -pbc cluster, -center tric and -ur 
compact (or without the latter two) produces a trajectory with the 
ligand in the correct position but some of the surface atoms of the 
protein jump between the boxes. If I then do trjconv with -fit 
progressive (or rot+trans) the protein is displayed as a whole but the 
ligand jumps out of the box. I've used the protein_heme_ligand group in 
the index file as the centering, clustering and fitting group.

And in all cases I see the weird angles at 50 deg, which are not shown 
in vmd visualising the system with ligand staying in the cavity.



Check out these cool words by Mark Abraham:
> 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.
> Mark
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