[gmx-users] Average Structure outputted from g_rmsf

[Arneh Babakhani]

Great, got it, thanks for the suggestion, appreciate the input,

Arneh

> 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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