AMBER Archive (2009)

Subject: [AMBER] B-factor

From: Cristina Sisu (
Date: Thu Oct 15 2009 - 12:04:25 CDT

Hello Amber users,

I know that lots has already been discussed about the b-factor, but I've
noticed some strange behaviour when calculating the b-factor with ptraj.
If I ask to calculate just the bfactor without calculating previously
the rms I obtain some very strange/huge values for the b-factor. More
exactly the input file looks like:

> trajin ./prod-run.mdcrd
> center origin
> atomicfluct out bf-prot1.res :1-127 byres bfactor
However when I calculate first the rms the values are completely different.
> trajin ./prod-run.mdcrd
> center origin
> rms first out prot1.rms time 10 @CA
> atomicfluct out bf-prot1.res :1-127 byres bfactor
The two answers are completely different. I am not sure why is so. I
know that b-factor is calculated as 8/3*p^2*fluct, but aren't the two
actions done independently?


AMBER mailing list