Hi,
I am using ptraj to calculate B-factor from 3 ns
MD done with AMBER 7.
---------------------------------------
trajin je_prodcor_1.mdcrd.gz
rms first out wt1md:1-198.CA
atomicfluct out back.apf.rms .CA byatom bfactor
--------------------------------------------
However, the calculated B factor is couple of times
higher than that of the crystal structure.
I thought generally B factors from MD is lower than
that in crystal structure. Is it always true? If not
what could be source of error in my MD (rmsd from
the crystal structure for CA atoms is about 1.2 Angs)?
Pradipta
==============================================
This Mail was Scanned for Virus and found Virus free
==============================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue Jun 22 2004 - 13:53:00 PDT
