Hello everybody,
I have calculated the RMSD of a protein which consists of 991 residues for
20ns in two ways.
1) I have considered the whole protein at once
For example
rms reference out totalprotein.dat :1-991.N,CA,C time 1
2) I have calculated the RMSD separately for each residue over the 20ns
period
For example
rms reference out residue1.dat :1 time 1
rms reference out residue2.dat :2 time 1
rms reference out residue3.dat :3 time 1
rms reference out residue4.dat :4 time 1
rms reference out residue5.dat :5 time 1
.............................................................
...............................................................
rms reference out residue991.dat :991 time 1
Then I calculated the average of the values given by 1) which was a single
value around 3.2 angstrom
Then I calculated the average of each individual residue using the output
of 2) which give 991 average values most of which are around or below 1
angstrom (non of them above 3.2)
* I was wondering If the whole protein had an average RMSD of 3.2 angstrom
why wouldn't the average RMSD of individual residues be close to the 3.2
mark?*
*
*
This might sound like a silly question but your response is highly
important to me.
Thank you
Sajeewa Dewage
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Received on Sat Oct 15 2011 - 09:30:03 PDT
