I am sending this mail again even a little idea would guide me.
I have seen RCSB structures where theres a B factor value ranging from
20-60.I dont know the unit but someone suggested thst it is Armstrong square
but what does these high value imply.(because if we take the square root its
still 4-9 Angstrom).Does the crystal structure coordinates are so uncertain.
When I run MD simulation while heating and equilibrating there is change of
1.5-2 Angstrom in RMSD.IS that fine even if I run on crystal structure there
is change and in that course the ligand moloecule loses some of the
interaction and I get slightly lesser binding affinity due to the lateral
shift of ligand molecule and the protein.Also sometimes it is proposed that
we should dock the ligand after running a small simulation.
On emore thing if I do homology modeling with 70% similarity i get a
structure of 0.3 Angstrom from the crystal structure but when I run the
simulation while heating and equilibrating the structure I get has 2
Angstrom from the crystal structure.
So is this normal or shall I change the protocol for better understanding
and please guide me bit more about the application of B factor.What are the
other things that I can analyze with the MD simulation data besides
energy,RMSD, inter atomic distances,B factor etc.
I am eagerly waiting for the replies.
Thanks in advance.
Regards
Shandilya Ashutosh
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Received on Fri Sep 24 2010 - 21:30:03 PDT
