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.
Regards,
Sampo
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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