Re: [AMBER] Ptraj B Factor PDB

From: Jason Swails <>
Date: Mon, 15 Jul 2013 14:06:42 -0400

On Mon, Jul 15, 2013 at 11:52 AM, Parker de Waal

> Hi Everyone!
> I'd like to map the b factors obtained from ptraj to the pdb of my original
> protein to visualize regions of higher flexibility. Can this be done in
> ptraj?
> My current input is as follows:
> trajin
> average bfac.pdb pdb
> atomicfluct out RMSF.dat :1-465 byres bfactor

This needs to be done in two stages. You need to first create an average
PDB (don't forget to do an RMS fitting first, or the average will include
contributions from rotation and translation). Then you have to run ptraj
again doing an RMS fit to the average PDB you just created.

Then the atomicfluct command will work. Note, though, that the
experimental definition of what a "B-factor" is is not the same as what
you're computing. They are related via an assumption that is made.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Mon Jul 15 2013 - 11:30:03 PDT
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