Hi,
I'm a beginner of xplor-nih. I'm trying to calculate the rmsd of the
structure generated by xplor-nih calculation and published x-ray structure.
I have tried both the script rmsdplot.inp (in
xplor-nih-2.23/tutorial/geomanal/) and the script targetRMSD.in (in the
xplor-nih-2.23/bin).
However, every time it reports error when I compare the calculated structure
and x-ray structure of my protein.
Before running the program for my own protein, I practiced the example in
xplor-nih-tutorial-2009/gb1_simple, in which how to get the rmsd between
calculated structure and x-ray structure is shown.
I found the g-xray.pdb file here has exactly the same atom definitions with
the calculated structure files in precalc/.
My question is:
All the published x-ray pdb files of my protein defines less atoms
(They do not have Hs) in each residue than the xplor-nih generated pdb
files. But, I think we chose C, CA and N for the comparison, so the program
should not read other atoms like Hs. But it always shows error when reading
the pdb file. Should I make these two pdb files include the same amount of
atoms for each residue? Or how can I modified the script targetRMSD.in to
make it work?
Thank you!
Best
Si
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