Because it uses the atom index, which is most likely NOT the same as your
processed file will not contain certain hydrogens, which are present in A.pdb.
24 aug 2012 kl. 16.33 skrev Hsinlin:
Thank you for your reply.
I checked the coordinates of all C-alpha atoms between two .pdb files.
They are exactly the same.
So I don't understand why g_rms(g_rmsdist) selecting group C-alpha give me
high values.
Sincerely yours,
Hsin-Lin
Erik Marklund wrote
Hi,
Since gromos-forcefields are not strictly all-atom forcefields, there
might be a mismatch between atoms in the two structures.
Best,
Erik
24 aug 2012 kl. 15.35 skrev Hsin-Lin Chiang:
Hi,
For example, I have a A.pdb as a initial structure file.
And I just used pdb2gmx on it to generate another B.pdb file with
GROMOS96 43a1 as its force filed.
Then I select C-alpha atoms to calculate RMSD.
echo 3 | g_rms -f B.pdb -s A.pdb
I suppose the RMSD value should be 0, but the value is high to about
0.5nm.
Can someone explain for me?
Sincerely yours,
Hsin-Lin
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