On Wed, Dec 3, 2014 at 1:49 PM, George Tzotzos <gtzotzos.me.com> wrote:
> 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
>
In 1 and 2 you are aligning residues 118 to 125. In 3 you are aligning
residues 18 to 125.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Dec 03 2014 - 11:30:02 PST
