[Chimera-users] Occupancy clusters

Yasser Almeida yasser.almeida at gmail.com
Tue Mar 16 01:38:24 PDT 2021


I want to do an occupancy analysis of a rigid ligand in a MD trajectory. I
used the MD Movie > Analysis > Calculate occupancy tool, and obtained the
volume maps of each heavy atom of the ligand. To check, I also used the gmx
spatial tool from GROMACS and the VolMap from VMD, to obtain the grids for
the whole ligand, which have basically the same shape.

This grid has a characteristic shape showing that particular orientations
are stable through the MD run. I want to extract representative structures
of these orientations, something like an "occupancy clustering". Note that
I say orientations and not conformations. Since the ligand is rigid, there
is no point to calculate the RMSD. So, what I want is to calculate clusters
of orientations of the ligand in the binding site.

Is this possible with Chimera?

Thanks in advance,
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