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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