Thanks a lot! Rafi!
>From: "Rafi Ahmad" <Rafi.Ahmad.fagmed.uit.no>
>Reply-To: amber.scripps.edu
>To: <amber.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.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
>
>_________________________________________________________________
>No masks required! Use MSN Messenger to chat with friends and family.
>http://go.msnserver.com/HK/25382.asp
>
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber.scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber.scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
_________________________________________________________________
Learn English via Shopping Game, FREE!
http://www.linguaphonenet.com/BannerTrack.asp?EMSCode=MSN06-03ETFJ-0211E
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Feb 14 2007 - 06:07:48 PST
