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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Dec 03 2014 - 11:00:02 PST
