Mark wrote:
> Dmitri Dubov wrote:
>> 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?
> You should test your hypothesis with g_cluster by converting two such
> frames to a .pdb "trajectory" with trjconv, and then editing by hand to
> permute such a pair, and comparing the results before and after permutation.
- Yes, I sure have done it: g_rms calculates nonzero RMSD of distances between
initial and permuted structure.
>> (Actually it is a very simplified example of my problem. My need is in
>> clustering structures for system with many permutations.)
> It's hard to advise when we don't know your real objective. Do you want
> to cluster over fully solvated structures, but losing fixed-pair mapping
> of waters? If so, then that's going to require quite expensive
> permutation over all possible orders of waters to find the global
> minimum RMSD. Heuristics exist to find a close-to-minimum permutation,
> but guaranteeing global minima is hard.
> On the other hand, if you merely want to cluster with any waters in the
> docking sites permuted, and ignore the rest, then you may need to script
> g_dist using each water molecule as a group and a key atom in a docking
> site as a group in order to identify the water molecule(s) in the site.
> Then trjconv with the same index file and that info can write a
> trajectory with just the selected waters. Now you may merely need to
> permute over a handful of possibilities with g_rms, before finally
> writing the permuted selected waters + solute to a trajectory (with
> trjconv). This is now prepared for clustering with g_cluster - the
> waters are ordered such that fixed-pair mapping makes sense.
Thanks for your advice! g_dist + trjconv may be helpful...
> Mark
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Dmitri
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