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.
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