The second command gives the Bfactor of all atoms individually, but I want Bfactor by residue considering all atoms of residue not only the backbone.
Now I use the following command, I think it is correct, But I have to be confirm.
atomicfluct out bfactor-all.dat :1-794 byres bfactor
Plz help me out.
Another question, I have 7ns trajectory and I am calculating Bfactor for this trajectory. While the rmsd is less than 5 but the Bfactor is more than 1000 for each residues. Shall I am doing any mistake or there is some problem in my simulation.
best regards
sindrila
________________________________
From: Aron Broom <broomsday.gmail.com>
To: Sindrila Dutta banik <sindrila.duttabanik.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Tuesday, 26 February 2013 12:38 PM
Subject: Re: [AMBER] Problem related to the bfactor calculation
why is the second command not what you want?
On Tue, Feb 26, 2013 at 12:03 AM, Sindrila Dutta banik <sindrila.duttabanik.yahoo.com> wrote:
Dear all,
>I want to calculate the B-factor of all atoms of each residues.
>
>Now when I use:
>
>atomicfluct out bfactor-bb.dat .C,CA,N byres bfactor
>
>
>then it gives only the bfactor of backbone atoms of each residue and while I using the following command
>
>atomicfluct out bfactor-bb-16.dat :1-974 byatom bfactor
>
>
>it gives the bfactor of all atoms individually.
>
>What command should I use for this, Please let me know.
>
>With best regards
>sindrila
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>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Mon Feb 25 2013 - 23:30:02 PST
