[gmx-users] Calculating average of B-factor

[David van der Spoel]

Mark Abraham wrote:
>> 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...


Actually the reported output is the pdb file. What does the xvg file 
say, you need to give -od flag? Did you try without the -anisou flag?

Otherwise per residue B factors would probably be meaningful only if you 
compute the RMSF of the center of mass of each residue. You can not get 
this information from the atomic B-factors, what is plotted in the -od 
file is the linear average over all atoms in a residue.

> 
> Mark
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se