The distortion of a protein starting structure can result from various
reasons:
1- experimental determination of the structure: this include the
experimental
conditions (T, pH) as well as the crystal contacts if X-ray were used,
dynamics
of some part of the molecule if NMR.
2- the manner you solvate and equilibrate. Using position restrain on
the
heavy atoms of the protein first, and then on the Calphas is generally
a good
idea. The time you need to run those simulations depends on the
system. If
you see deviations you can try to run a bit longer. 100 ps is
generally sufficient
but can be extended to 500 ps, this is no problem.
3- the force field you are using might also trigger some "small"
deviations of the
protein. The protein structure might contain "strange" local
configuration that
are not sable in the FF.
4- you set up, meaning time step, temperature, pressure, ...
Note finally that a deviation from the starting structure might just
be a fluctuation
of a labile region of the protein ...
On Apr 15, 2010, at 8:40 AM, sonali dhindwal wrote:
Hello All,
I have a protein of 576 amino acid long, and has a barell shape
topolgy.
I have done MD simulation on it for 1ns, and my protein has got
distorted shape, i.e, one of the strand became coil and other
strands became small.
I wrote this query before also, can it be possible that this is due
to equilibration conditons i am giving, i am equilibrating it for
100 ps under NVT using brendenson coupling.
What should be ideal time for equibrating the protein with solvent ?
How should it be determined, or it is based on experimenting with
different conditions ?
Please help.
Regards.
--
Sonali Dhindwal
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