Arneh Babakhani wrote:
Hi,
When outputting the average structure from g_rmsf using the -ox option,
some of my residues in that average structure pdb have awkward coordinates
(when you visualize it in VMD, it looks very strange). Sometimes atoms
are placed very close to each other, with really bad bond angles. I
suppose this is a facet of the averaging scheme in g_rmsf.
Yes. If you ask for an not-necessarily-physical result, you usually get
one... see http://wiki.gromacs.org/index.php/Average_Structure
Is there a way to correct for this, and to obtain an averagestructure.pdb
that looks more reasonable coordinates and bond angles? (I ask b/c I'd
like to use this averagestructure.pdb in further studies, such as
docking.)
"Correcting for" is not quite the right phrasing here... :-) It's
already correct according to the algorithm you used... it's not the
algorithm's fault you actually wanted a physical structure. One approach
you can use is to select the structure with the smallest RMSD from the
average, kind of like selecting the median as the central measure rather
than the mean of a numerical data set. Or you can take the nonphysical
structure and do EM on it... One needs to apply brain, of course!
Mark
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