[gmx-users] b-factor

[Daniel Larsson]

On Oct 22, 2007, at 10:07, tangxuan wrote:

> Dear all,
>  I have got a pdb file by command g_rmsf and option -oq, and the  
> content
> of the file is like this:
> TITLE     Protein in water
> REMARK    THIS IS A SIMULATION BOX
> CRYST1  148.918  148.918  148.428  59.89  59.89  90.00 P 1           1
> MODEL        1
> ATOM  47354  CA  ALA I9967      60.915  88.765  42.075  1.00 92.09
> ATOM  47364  CA  GLY I9968      60.037  91.017  39.099  1.00 31.09
> ATOM  47371  CA  PHE I9969      59.892  94.727  38.149  1.00 13.34
> ATOM  47391  CA  LYS I9970      56.778  96.973  38.146  1.00 13.59
> ATOM  47413  CA  ALA I9971      57.412 100.730  38.292  1.00  8.88
> ATOM  47423  CA  GLY I9972      55.243 102.910  40.429  1.00  8.42
> ATOM  47430  CA  VAL I9973      55.349 104.629  43.777  1.00  6.96
> ATOM  47446  CA  LYS I9974      55.039 102.584  47.023  1.00 10.56
> ATOM  47468  CA  ASP I9975      53.919 102.844  50.642  1.00  8.59
> ATOM  47480  CA  TYR I9976      56.618 101.675  53.096  1.00  5.41
> ATOM  47501  CA  ARG I9977      54.179 100.074  55.607  1.00  6.66
> ATOM  47525  CA  LEU I9978      53.642  97.083  53.329  1.00 10.59
> ATOM  47544  CA  THR I9979      57.043  95.266  53.147  1.00 10.24
> ATOM  47558  CA  TYR I9980      59.307  96.919  55.730  1.00  4.74
> ATOM  47579  CA  TYR I9981      57.141  96.770  58.853  1.00  4.52
> ATOM  47600  CA  THR I9982      57.423  93.001  59.524  1.00  5.61
> ATOM  47613  CA  PRO I9983      55.634  91.722  62.707  1.00 11.23
> ATOM  47628  CA  ASP I9984      56.655  88.019  62.809  1.00 13.38
> ATOM  47640  CA  TYR I9985      60.439  88.728  62.349  1.00  9.58
> Could you tell me which column should be the b-factor?

It is the last column that contains the B-factor value.

> B-factor is the
> thermal deviation of the atom, and could you tell me how the gromacs
> gives the values of b-factor for each atom in detail?

Usually the B-factor can be viewed as an incertitude factor (between  
0-100). I'm not sure about the implementation in g_rmsf, but unless  
anyone else here on the list corrects me, I think you could assume  
this is what g_rmsf writes.

>
> Thank you!
>
>
> Tang Jiaowei
>
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