[gmx-users] Average Structure outputted from g_rmsf

[Arneh Babakhani]

Yes, that's what I'd like. great, thanks for the suggestion,

Arneh


> If you want a structure representative for your trajectory, rather
> than the average, I suggest using g_cluster to cluster your frames
> and take the cluster center from the largest cluster.
>
> /Erik
>
> 20 sep 2007 kl. 17.18 skrev 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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>>
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>
> _______________________________________________
> Erik Marklund, PhD student
> Laboratory of Molecular Biophysics,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,	75124 Uppsala, Sweden
> phone:	+46 18 471 4537		fax: +46 18 511 755
> erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys
>
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