[gmx-users] B-factor to large? Input for TLS

[Henri Mone]

Dear Gromacs Users and Experts,

I want to calculate from my xtc trajectory the B-factor and the
anisotropic temperature factor.  I'm using following gromacs command:

$ g_rmsf -f traj.xtc -o rmsf.xvg -oq bfac.pdb -ox bfac2.pdb -s structure.pdb

I want to input the resulting PDB file to the "TLS" Server [1] to
calculate the hinge residues for my system.
The B-factor which "g_rmsf" is calculating seem to be to large, they
are in the range of 2000 to 6000  (last column without the "1.00"
prefix) [2].
The website [3] suggests that a reasonable  B-factor should is in the
range of 21 to 200. Also the TLS server [1] complains that the
b-factors are in the wrong range. I did several test but I have no
idea what I"m doing wrong. The trajectory is with 250ns long enough to
get for my small system a convergence on the B-factor.
- I thought it could be a unit problem, what are the B-factor units
which "g_rmsf" uses? Could this cause such an huge difference in the
b-factor?
- What is the standard unit for the b-factor in the PDB definition
(from the PDB database)?
- What is a realistic range for the b-factor?
- What else could be the error source, what am I doing wrong?


Thanks, any help is welcome,
Henrey

---1: TLSMD SERVER
http://skuld.bmsc.washington.edu/~tlsmd/



---2: bfac2.pdb :
...
ATOM   6146  N   GLY   435      97.841  52.072  37.712  1.006712.85
ATOM   6147  HN  GLY   435      97.972  52.020  37.437  1.006676.79
ATOM   6148  CA  GLY   435      97.953  52.003  37.883  1.006739.30
ATOM   6149  HA1 GLY   435      97.975  51.822  37.563  1.006956.61
ATOM   6150  HA2 GLY   435      97.554  52.041  37.972  1.007042.78
ATOM   6151  C   GLY   435      98.601  52.111  38.350  1.006210.20
ATOM   6152  O   GLY   435      98.552  51.909  38.905  1.006278.92
ATOM   6153  N   ASN   436      99.235  52.437  38.127  1.005772.75
ATOM   6154  HN  ASN   436      99.262  52.602  37.668  1.005803.67
ATOM   6155  CA  ASN   436      99.904  52.574  38.508  1.005343.12
ATOM   6156  HA  ASN   436      99.947  52.400  38.918  1.005671.18
ATOM   6157  CB  ASN   436     100.537  52.527  37.948  1.005355.63
ATOM   6158  HB1 ASN   436     100.960  52.556  38.127  1.005098.00
ATOM   6159  HB2 ASN   436     100.553  52.657  37.601  1.005272.78
ATOM   6160  CG  ASN   436     100.587  52.258  37.586  1.006031.62
ATOM   6161  OD1 ASN   436     100.582  52.138  37.675  1.006435.18
ATOM   6162  ND2 ASN   436     100.641  52.163  37.176  1.006306.09
ATOM   6163 1HD2 ASN   436     100.689  51.993  36.928  1.006834.63
ATOM   6164 2HD2 ASN   436     100.652  52.264  37.117  1.006062.64
ATOM   6165  C   ASN   436      99.947  53.023  38.917  1.004590.56
ATOM   6166  O   ASN   436      99.651  53.240  38.597  1.004290.70
...

---3: B-factor range at 3 Å resolution
http://www.p212121.com/2009/04/12/b-factor-range-3-resolution/