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
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.
I'm using Gromacs 3.3.1 on an Ubuntu 7.04.
Any help is appreciated!
Sampo
________________________
Sampo Karkola
Doctoral student
Laboratory of Organic Chemistry
Department of Chemistry
POBox 55, FIN-00014
University of Helsinki
Finland
tel. +358 9 191 50369
fax. +358 9 191 50366
[EMAIL PROTECTED]
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