[gmx-users] b-factor

[Erik Marklund]

leila karami skrev:
> Hi all
>  
> pdb file for my protein was obtained by solution NMR. this file is as 
> follows :
>  
> ATOM      1  N   GLY A   1     -25.349  -8.577   4.055  1.00  0.00
> ATOM      2  CA  GLY A   1     -24.037  -8.099   4.448  1.00  0.00
> ATOM      3  C   GLY A   1     -23.580  -6.913   3.622  1.00  0.00
> ATOM      4  O   GLY A   1     -23.652  -6.939   2.393  1.00  0.00
> ATOM      5  H1  GLY A   1     -26.109  -7.957   4.035  1.00  0.00
> ATOM      6  HA2 GLY A   1     -24.067  -7.811   5.488  1.00  0.00
> ATOM      7  HA3 GLY A   1     -23.324  -8.902   4.328  1.00  0.00
> ATOM      8  N   SER A   2     -23.111  -5.869   4.298  1.00  0.00
>  
> pdb file obtaind from g_rmsf  -f  pr.xtc  -s  pr.tpr  -n  pr.ndx -oq 
> command is as follws :
>  
> ATOM      5  CA  NGL     1      20.794  51.547  38.010  1.00 272.65
> ATOM     12  CA  SER     2      23.444  51.157  35.390  1.00 257.41
> ATOM     23  CA  SER     3      25.254  48.487  33.290  1.00 189.09
> ATOM     34  CA  GLY     4      28.474  47.777  31.510  1.00 114.27
> ATOM     41  CA  SER     5      27.814  48.657  27.860  1.00 195.51
> ATOM     52  CA  SER     6      31.164  48.167  26.020  1.00 217.99
> ATOM     63  CA  GLY     7      31.934  49.987  22.770  1.00 300.70
> ATOM     70  CA  LYP     8      32.204  48.057  19.510  1.00 248.64
>  
> so can I compare experimental B-factor with that calculated from MD?
>  
> any help will highly appreciated. 
I'm currently calculating b-factors too, and there may be two things 
that you must think about. One is, as I understand it, that the b-factor 
in x-ray scattering experiments is unaffected by motions in the 
scattering directoion, effectively reducing the observerd mds of the 
atoms so that B = pi^2 * 8 * msd_p, where msd_p is only the motions 
perpendicular to the scattering direciton. Another thing to consider is 
wether isotropic b-factors is suitable in your case.

Erik

-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/