Dear GMX'ers,
Many gmx tools (g_rms, g_rmsdist, g_cluster etc.) calculate RMSD of distances.
Take some molecule having two docking sites (A and B) and hydrated with two
water molecules (C and D). Let's inspect two structures realized. The first
structure is with C docking to A and D to B, and the 2nd one has C docking to B
and D to A. These structures have large RMSD of distances between FIXED PAIRS
OF THEIR ATOMS, and to my knowledge g_cluster will differ them. How can I
cluster these structures?
(Actually it is a very simplified example of my problem. My need is in
clustering structures for system with many permutations.)
--
уBest regards,
Dmitri mailto:[email protected]
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