[gmx-users] b-factor

[leila karami]

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.
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