[gmx-users] Calculating average of B-factor
David van der Spoel
spoel at xray.bmc.uu.se
Sat May 3 19:16:32 CEST 2008
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
>
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--
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
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