Hi,
problem solved and it was a stupid mistake by me. The reference
structure I used (the -s option in trjconv) had the ligand out of the
active site. When I selected another reference with proper positioning
of the system, everything went well. Thanks anyway!
Sampo
Check out these cool words by Mark Abraham:
Sampo Karkola wrote:
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.
Well, find out what frames have these occurring and see why it is.
Mark
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