thank you for your reply! my simulation is at 300K. the experimental
bfactors is lower than the calculated ones in 20~30Å, is it normal?
in a paper, the calculated bfactor is high than the experimental ones,
the author said the high resolution of the crystal structure make it
happen. in my case, the crystal structure is 2.0Å, is that enough
high?
On 8/7/05, Carlos Simmerling <carlos.ilion.bio.sunysb.edu> wrote:
> is your simulation at the same temperature as the xray experiment?
> only then would you expect thermal fluctuations to have the
> same magnitude. also, unless you simulate the crystal you cannot expect
> the same fluctuations.
>
> haixiao jin wrote:
>
> >It is said that the crystallographic B-factor measures both the
> >thermal fluctuation (including conformational heterogeneity of
> >proteins) and global translation and rotation. In our calculation
> >B-factors, however, the global translation/rotation has been removed
> >by rigid-body alignment. Therefore, one might expect that the
> >calculated B-factors should be smaller than the experimental ones.
> >But the calculated B-factors I have obtained are larger than the
> >experimental ones. Here in my bfactor.in file.
> >
> >Bfactor.in:
> >
> >trajin 1npt.mdcrd
> >reference min.pdb
> >center :1-373 origin mass
> >image origin center familiar
> >rms reference out protein.out :1-372.CA
> >rms reference out ligand.out :373
> >atomicfluct out bfactor.out .CA byatom bfactor
> >
> >Is that anything wrong with my bfactor.in? thank you for your suggestion!
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>
> --
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Associate Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
> Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
> ===================================================================
>
>
>
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Received on Mon Aug 08 2005 - 06:53:00 PDT
