[gmx-users] Calculating average of B-factor

[Mark Abraham]

> Dear GROMACS users and developers,
> Sorry for posting same topic again. I really appreciate those replies,
> thank you. I did use the -res option so i can get the plot rmsf (nm) vs
> residue. However, with -res option, the bfac.pdb produced include the
> ANISOU line for each atom (whish is the anistropic temperature
> factor). The B-factor is still at the end of each atom line.
> My question is, how can I calculate the average of each residue? here's
> few line i took form the bfac.pdb:TITLE     Protein in water
> REMARK    THIS IS A SIMULATION BOX
> CRYST1   90.072   90.010   90.061  70.58 109.50  70.49 P 1           1
> MODEL        1
> ATOM      1  N   ALA     1      39.870  49.598  31.575  1.00  0.00
> ANISOU    1  N   ALA     1    27382  16872  28413  -5818 -15784  -6247
> ATOM      2  H1  ALA     1      40.270  50.118  30.815  1.00  0.00
> ANISOU    2  H1  ALA     1    36121  21080  32250  -8317 -17149  -8021
> ATOM      3  H2  ALA     1      40.080  48.628  31.485  1.00  221.02
> ANISOU    3  H2  ALA     1    32407  19879  31690  -6481 -17864
> -7202ATOM      4  H3  ALA     1      38.870  49.728  31.575  1.00  218.06
> ANISOU    4  H3  ALA     1    33154  18573  31125  -6794 -16678  -6289
> ATOM      5  CA  ALA     1      40.500  50.098  32.805  1.00  168.66
> ANISOU    5  CA  ALA     1    17671  18590  27822  -3239 -12795  -8333
> ATOM      6  CB  ALA     1      39.990  49.098  33.845  1.00  220.77
> ANISOU    6  CB  ALA     1    15699  36171  32009 -10813  -7176 -10100
>
> Can I just average the (B-factor) value at each end of atom line for each
> residue?
> Its okay if the B-factor vs redisue plot cant be build. I can use the
> B-factor vs atoms plot. But people (in papers) have done it (B-fac vs res)
> before with GROMACS and I'm eager to see the plot for my protein :)

Well, you can start by writing out the mathematical expression for
per-residue B-factor and form your own opinion on whether it means
anything. You'll have to defend your opinion to do any analysis worth
doing, so you should start thinking sooner rather than later.

Quite possibly a reported per-residue B-factor could be based only on data
for only one atom per residue, but you'd have to read the papers to tell
that...

Mark