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 Post subject: Log file RMSD question
PostPosted: Fri Sep 13, 2013 2:31 pm 
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Joined: Tue Mar 15, 2011 7:36 pm
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Hi,

I cannot say that I am a "new user" but so far I have not been paying much attention to the following output in the log file:

dist from best mode
rmsd l.b | rmsd u.b

I was trying to understand the significance of it but failed. Somehow now that I am writing this question things clear up a bit. Still, so the term mode refers to solution. The best solution obviously has 0.0 rmsd to itself. The 2nd best structure (mode) is then reported to have a rmsd to #1 calcuated between pairs of atoms with the same name for the "upper bounds" rmsd and the nearest atom of the same type (say nearest carbon atom even if the names don't match) for the lower bounds value. While the latter value may be odd it is useful in cases of phenyl rings that rotate 180 deg with CD1<->CD2, CE1<->CE2 swaps (forgive my use of "protein chemistry" nomenclature!) but in essence this is still the "same" conformation and deserves to be reported to have a low rmsd to the top solution.

So when do solutions are considered to be the same within vina? Does vina cluster solutions actually i.e. if it gets 10 solutions that are close to say -10 kcal/mol and are within some max value of rmsd - are those solutions considered the same and appear only once in the long file?
Do people report rmsd values between solutions as a means by which the quality of the top solution can be judged - and if so how can it be judged?

Ah one more thing: I am comparing crystal structure ligands with vina docking solutions - for the most part they are very close. But I am looking for a program that can automatically calculate rmsd between a ligand from a crystal structure and a solution from vina with preferably no user intervention. I can do this in O but it seems a bit tedious - in addition I would like to have a program that is smart enough to figure simple torsions out (in the spirit of lower bound rmsd). Is there such a program?

Comments are welcome.

Thanks,

Lothar


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