BETA = 8pi^2/3 RMSD^2
:)
you may be missing a factor here
Ed
Ashutosh Shandilya wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Sep 25 2010 - 11:30:03 PDT
