AMBER Archive (2007)

Subject: RE: AMBER: atomicfluct

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Tue Feb 13 2007 - 21:36:35 CST


Thanks a lot! Rafi!

>From: "Rafi Ahmad" <Rafi.Ahmad_at_fagmed.uit.no>
>Reply-To: amber_at_scripps.edu
>To: <amber_at_scripps.edu>
>Subject: RE: AMBER: atomicfluct
>Date: Mon, 12 Feb 2007 09:32:37 +0100
>
>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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