[gmx-users] Average Structure outputted from g_rmsf

[Arneh Babakhani]

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.)

thanks,

Arneh