AMBER Archive (2007)

Subject: RE: AMBER: atomicfluct

From: Rafi Ahmad (Rafi.Ahmad_at_fagmed.uit.no)
Date: Mon Feb 12 2007 - 02:32:37 CST

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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of Catein Catherine
Sent: 12. februar 2007 06:46
To: amber_at_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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