I wrote g_spatial and it should produce a spatial distribution
function. However, it's rather complicated to use. Did you follow the
directions in g_spatial -h ? There are about 10 steps to use it. It is
so complicated on purpose in order to give the user full flexibility,
but this means that you need to do all of your alignment yourself. If
you did that correctly, then I also suggest that you should make sure
that you are visualizing it correctly in VMD. By default you will see
some atoms, but that is only there because VMD will not recognize a
gaussian cube without any atoms, and also it makes it easier for you
to ensure that any other pdbs you may load overlay correctly.
Therefore ensure that you switch the representation to isosurface and
then slide the bar so that you see the appropriate isosurface contour.
Please report back to the list with findings so that other users can
later benifit from your work
Chris.
Gadzikano Munyuki wrote:
I want to analyse the solvent around a peptide . I used g_sdf and
the output that i am getting (i.e the refmol.gro) does not have the
whole peptide molecule but just the residues that i use to define
the coordinate system . I then tried to use g_spatialbut its doing
something very different and not spatial distibution, it looks like
its executing g_cluster instead. I was wondering if g_custer and
g_spatial are meant to do the same thing.
Have a read of g_cluster -h and g_spatial -h and decide whether they're
doing the same thing :-)
Mark
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