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

[Henri Mone]

Hi Mark,

Thanks for your reply. I will check if the reference structure and the
trajectory fit.

Cheers
Henrey

On Mon, Nov 7, 2011 at 9:15 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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/