SDF and occupancy clusters

User discussions
1

GROMACS version: 2020.1
GROMACS modification: No

Hello,

I used gmx spatial to obtain the SDF of a rigid ligand in a binding site. The volume map is very revealing and clearly shows some stable orientations of the ligand after the sampling. Now, I want to extract representative structures of this complex, as occupancy clusters. Since the ligand is quite rigid and tumbles in the binding site, gmx cluster wouldn’t be the proper tool.

Is there any tool that extract representative structures of the SDF? I saw the -w option of gmx spatial, but it doesn’t write anything.

Thanks in advance,
-Yasser

2

-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
Maybe you need to write view which one