[gmx-users] non-existent angles found from trajectory g_angle
sampo.karkola at helsinki.fi
Fri Oct 12 09:57:25 CEST 2007
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.
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