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

[Mark Abraham]

On 5/11/2011 11:05 AM, Henri Mone wrote:
> 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

Does this reference structure in -s make sense for the trajectory 
supplied for -f? If the computed atomic deviations make no sense, then 
neither will the fluctuations. I have no idea if g_rmsf takes proper 
account of periodicity, but you might need either to massage the 
trajectory suitably with trjconv (see website for suggested workflows), 
or supply a .tpr with the correct box information.

> 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?

g_rmsf converts to Angstroms before writing B-factor output to PDB, as 
you would expect.

Mark

> - 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/