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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 23 2015 - 06:00:07 PST
