Well, in your atomicfluct command you have the mask .CA which means all C alphas.
Best
Vlad
On February 23, 2015 2:30:04 PM CET, George Tzotzos <gtzotzos.me.com> wrote:
>I’m dealing with a homo-dimer complex, ChainA residues: 1-125, ChainB
>residues 127-251
>
>I’m trying to calculate B-factors for the backbone CA of chains A and
>B.
>
>I’m using the following script
>
>parm 4fqt_solv.prmtop
>trajin prod_0-100ns.nc
>rms first mass out rmsd_first.dat :18-125.CA
>atomicfluct out bfactor.apf .CA byres bfactor
>run
>xmgrace bfactor.apf
>
>The output I obtain does not correspond to the residues specified in
>the mask. Instead, I obtain CA B-factors for all 250 residues.
>
>INPUT: Reading Input from file rmsf_bfactor.in
> [parm 4fqt_solv.prmtop]
> AmberParm Title: [default_name]
> Radius Set: H(N)-modified Bondi radii (mbondi2)
> [trajin prod_0-100ns.nc]
> [prod_0-100ns.nc] contains 10000 frames.
> [rms first mass out rmsd_first.dat :18-125.CA ]
>RMSD: (:18-125.CA), reference is first frame (:18-125.CA), with
>fitting, mass-weighted.
> [atomicfluct out bfactor.apf @CA byres bfactor]
> ATOMICFLUCT: calculating B factors, output to file bfactor.apf
> Atom mask: [@CA]
> Start: 1 Stop: Final frame
> [run]
>
>PARAMETER FILES:
>0: 4fqt_solv.prmtop, 48547 atoms, 15103 res, box: Trunc. Oct., 14855
>mol, 14833 solvent, 10000 frames
>
>INPUT TRAJECTORIES:
>0: [prod_0-100ns.nc] is a NetCDF AMBER trajectory, Parm
>4fqt_solv.prmtop (Trunc. Oct. box) (reading 10000 of 10000)
> Coordinate processing will occur on 10000 frames.
>
>ACTION OUTPUT:
> ATOMICFLUCT: Calculating fluctuations for 10000 sets.
>
>DATASETS:
> 2 data sets:
> RMSD_00000 "RMSD_00000" (double), size is 10000
> Fluct_00001 "Fluct_00001" (double), size is 250
>DATAFILE OUTPUT:
> rmsd_first.dat: RMSD_00000
> bfactor.apf: Fluct_00001
>rmsd_first.dat: Writing 10000 frames.
>bfactor.apf: Writing 251 frames.
><<<<<<<<<--------------------------------
> [xmgrace bfactor.apf]
>
>
>Any suggestions regarding this behavior will be much appreciated.
>
>Regards
>
>George
>
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Received on Mon Feb 23 2015 - 06:00:09 PST
