[gmx-users] Calculating average of B-factor

[Alif M Latif]

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 :) 

"May the Force Fields be with You" - GROMACS Wars
 
Muhammad Alif Mohammad Latif

Department of Chemistry
Faculty of Science
Universiti Putra Malaysia
43400 UPM Serdang, Selangor
MALAYSIAComments, advices and suggestions are greatly appreciated. Thank You.


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