[AMBER] B-factor values

From: George Tzotzos <gtzotzos.me.com>
Date: Wed, 03 Dec 2014 15:49:28 -0300

I used the following input files to obtain b-factors for the backbone atoms of a protein after a 100ns MD simulation,

1. Reference: average structure

trajin prod_100ns.nc
reference av.pdb
rms reference out rms.dat :118-125.CA
atomicfluct out bfactor.dat :18-125.CA byres bfactor

2. Reference: minimisation output

trajin prod_100ns.nc
reference min.rst
rms reference out rms.dat :118-125.CA
atomicfluct out bfactor.dat :18-125.CA byres bfactor

3. Reference: first snapshot of the trajectory

trajin prod_100ns.nc
rms first mass out rmsd_first.dat :18-125.CA
atomicfluct out bfactor.apf :18-125.CA byres bfactor

The values obtained for 1 and 2 are identical. For 3 an order of magnitude less (see attached snapshot). In addition the values of the temp-factor of the X-ray model much closer to 3, above.

I’d appreciate any suggestions regarding this difference in values

Thanks in advance

George



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Received on Wed Dec 03 2014 - 11:00:02 PST
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