leila karami skrev:
Hi all
pdb file for my protein was obtained by solution NMR. this file is as
follows :
ATOM 1 N GLY A 1 -25.349 -8.577 4.055 1.00 0.00
ATOM 2 CA GLY A 1 -24.037 -8.099 4.448 1.00 0.00
ATOM 3 C GLY A 1 -23.580 -6.913 3.622 1.00 0.00
ATOM 4 O GLY A 1 -23.652 -6.939 2.393 1.00 0.00
ATOM 5 H1 GLY A 1 -26.109 -7.957 4.035 1.00 0.00
ATOM 6 HA2 GLY A 1 -24.067 -7.811 5.488 1.00 0.00
ATOM 7 HA3 GLY A 1 -23.324 -8.902 4.328 1.00 0.00
ATOM 8 N SER A 2 -23.111 -5.869 4.298 1.00 0.00
pdb file obtaind from g_rmsf -f pr.xtc -s pr.tpr -n pr.ndx -oq
command is as follws :
ATOM 5 CA NGL 1 20.794 51.547 38.010 1.00 272.65
ATOM 12 CA SER 2 23.444 51.157 35.390 1.00 257.41
ATOM 23 CA SER 3 25.254 48.487 33.290 1.00 189.09
ATOM 34 CA GLY 4 28.474 47.777 31.510 1.00 114.27
ATOM 41 CA SER 5 27.814 48.657 27.860 1.00 195.51
ATOM 52 CA SER 6 31.164 48.167 26.020 1.00 217.99
ATOM 63 CA GLY 7 31.934 49.987 22.770 1.00 300.70
ATOM 70 CA LYP 8 32.204 48.057 19.510 1.00 248.64
so can I compare experimental B-factor with that calculated from MD?
any help will highly appreciated.
I'm currently calculating b-factors too, and there may be two things
that you must think about. One is, as I understand it, that the b-factor
in x-ray scattering experiments is unaffected by motions in the
scattering directoion, effectively reducing the observerd mds of the
atoms so that B = pi^2 * 8 * msd_p, where msd_p is only the motions
perpendicular to the scattering direciton. Another thing to consider is
wether isotropic b-factors is suitable in your case.
Erik
--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
[email protected] http://folding.bmc.uu.se/
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