[gmx-users] non-existent angles found from trajectory g_angle
sampo.karkola at helsinki.fi
Fri Oct 12 11:25:49 CEST 2007
I have another trajectory with the same enzyme but another ligand with
exactly the same parameters and boxtype and simulated with the same
version of Gromacs and with the same machine at the same time. With this
one everything seems to work fine with g_angle and I also get correct
visualisation with trjconv -pbc cluster -center tric -ur compact and
trjconv -fit progressive.
I can't figure out what is causing the problem in the first one.
Check out these cool words by Sampo Karkola:
> 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.
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