Hi Catherine,
I am also doing the same thing.
For the DNA atomic fluctuations you have to mention the backbone atoms
of DNA like you have done for the protein. The Y axis will be the RMSB
and the X-axis will be your residue number as in the pdb file from which
you made the prmtop and inpcrd file.
Something like this:
atomicfluct out test.apf .CA,C,N,P,O3',O5',C3',C4',c5' byres
Hope this helps.
Rafi
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
Of Catein Catherine
Sent: 12. februar 2007 06:46
To: amber.scripps.edu
Subject: AMBER: atomicfluct
Dear All,
I could like to calculate the atomic fluctuation per residues for a
protein-DNA complex.
It seems to me that I could use the following command line in ptraj for
this
purpose:
atomiclfluct out test_mdcrd.apf .C, CA, N byres bfactor
However, I cannot find the results for DNA residues, and the unit of the
atomic fluctuation is not known, as it is very large. What is the unit
for
the y-axis? Can I convert them into A unit instead?
Did I do anything wrong here? Could you mind to instruct me how to
improve
the command lines used?
Best regards,
Catherine
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Received on Wed Feb 14 2007 - 06:07:18 PST
