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<p>Mark wrote:</p>
<p><br></p>
<p><span class=rvts6>> Dmitri Dubov wrote:</span></p>
<p><span class=rvts7>>> Dear GMX'ers,</span></p>
<p><br></p>
<p><span class=rvts7>>> 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?</span></p>
<p><br></p>
<p><span class=rvts6>> You should test your hypothesis with g_cluster by converting two such </span></p>
<p><span class=rvts6>> frames to a .pdb "trajectory" with trjconv, and then editing by hand to</span></p>
<p><span class=rvts6>> permute such a pair, and comparing the results before and after permutation.</span></p>
<p><br></p>
<p>- Yes, I sure have done it: g_rms calculates nonzero RMSD of distances between initial and permuted structure.</p>
<p><br></p>
<p><span class=rvts7>>> (Actually it is a very simplified example of my problem. My need is in clustering structures for system with many permutations.)</span></p>
<p><br></p>
<p><span class=rvts6>> It's hard to advise when we don't know your real objective. Do you want</span></p>
<p><span class=rvts6>> to cluster over fully solvated structures, but losing fixed-pair mapping</span></p>
<p><span class=rvts6>> of waters? If so, then that's going to require quite expensive </span></p>
<p><span class=rvts6>> permutation over all possible orders of waters to find the global </span></p>
<p><span class=rvts6>> minimum RMSD. Heuristics exist to find a close-to-minimum permutation,</span></p>
<p><span class=rvts6>> but guaranteeing global minima is hard.</span></p>
<p><br></p>
<p><span class=rvts6>> On the other hand, if you merely want to cluster with any waters in the</span></p>
<p><span class=rvts6>> docking sites permuted, and ignore the rest, then you may need to script</span></p>
<p><span class=rvts6>> g_dist using each water molecule as a group and a key atom in a docking</span></p>
<p><span class=rvts6>> site as a group in order to identify the water molecule(s) in the site.</span></p>
<p><span class=rvts6>> Then trjconv with the same index file and that info can write a </span></p>
<p><span class=rvts6>> trajectory with just the selected waters. Now you may merely need to </span></p>
<p><span class=rvts6>> permute over a handful of possibilities with g_rms, before finally </span></p>
<p><span class=rvts6>> writing the permuted selected waters + solute to a trajectory (with </span></p>
<p><span class=rvts6>> trjconv). This is now prepared for clustering with g_cluster - the </span></p>
<p><span class=rvts6>> waters are ordered such that fixed-pair mapping makes sense.</span></p>
<p><br></p>
<p>Thanks for your advice! g_dist + trjconv may be helpful...</p>
<p><br></p>
<p><span class=rvts6>> Mark</span></p>
<p><span class=rvts6>> _______________________________________________</span></p>
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<p><span class=rvts6>> Please search the archive at </span><a class=rvts8 href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class=rvts9> before posting!</span></p>
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<p><br></p>
<p>Dmitri</p>
<p><a class=rvts11 href="mailto:ddubov@ngs.ru"><br></a></p>
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