Hi,
On Mon, Feb 23, 2015 at 6:30 AM, George Tzotzos <gtzotzos.me.com> wrote:
> atomicfluct out bfactor.apf .CA byres bfactor
>
Vlad is correct - '.CA' selects *all* alpha carbons. if you only want
residues 18-125 you need something like ':18-125.CA'. Also, specifying
'byres' with a mask like '.CA' is not useful, since you're only selecting
one atom from each residue anyway. It's better to do something like
':18-125.CA' or ':18-125 byres'.
-Dan
> 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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>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Feb 23 2015 - 08:00:02 PST
