[gmx-users] Average Structure outputted from g_rmsf

[Arneh Babakhani]

Ok, thanks, I figured as much, was wondering if there was an option
perhaps in g_rmsf that would produce a "minimized" average structure . . .
I guess not,

Arneh



> 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
>
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