Hi Jason,
Thank you for the response, I believe I understand the steps required
however I do not know how to perform the the RMS fit to the average pdb.
Here are my two tenative *.ptraj files
step1.ptraj:
trajin density_extend.nc # load density trajectory
rms first :1-465.CA # rms first to the first frame for
CA
average step_1_average.pdb pdb # output the average pdbfile
step2.ptraj
???? somehow load the average pdb?
rms first 1-465.CA
atomicfluct out rmsf_data.dat :1-465.CA byres bfactor
I hope this is close...
Parker
On Mon, Jul 15, 2013 at 2:06 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Mon, Jul 15, 2013 at 11:52 AM, Parker de Waal
> <Parker.deWaal09.kzoo.edu>wrote:
>
> > 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 density_extend.nc
> > 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.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Mon Jul 15 2013 - 11:30:03 PDT
