[gmx-users] Average Structure outputted from g_rmsf

[Florian Haberl]

Hi,

On Thursday, 20. September 2007 16:15, 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.
>
> 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.)

this is the normal problem, when looking at average structures. Easiest is to 
minimize the structure again, depends on your strucure you have perphaps to 
restrain backbone atoms.

>
> thanks,
>
> Arneh
>
>
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Greetings,

Florian

-- 
-------------------------------------------------------------------------------
 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
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 Telephone:  	+49(0) − 9131 − 85 26581
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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