> > Thank you for the response, I believe I understand the steps required
> > however I do not know how to perform the the RMS fit to the average pdb.
> >
> > Here are my two tenative *.ptraj files
> >
> > step1.ptraj:
> > trajin density_extend.nc # load density trajectory
> > rms first :1-465.CA # rms first to the first frame
> > for
> > CA
> > average step_1_average.pdb pdb # output the average pdbfile
> >
> > step2.ptraj
> > ???? somehow load the average pdb?
> >
>
> Look for the "reference" command. This will load a reference structure.
An alternative trick is to simply load up the PDB first:
trajin avg.pdb
trajin density_extend.nc
rms first mass out rms :1-465.CA
^
need residue designator
so step1
trajin density_extend.nc
trajout avg.pdb pdb
rms first mass out rms :1-465.CA
step2
trajin avg.pdb
trajin density_extend.nc
rms first mass out rms :1-465.CA
atomicfluct out bfactor.dat :1-465 bfactor
(and you can look by atom or by residue with the fluctuations)
--tec3
p.s. if you look on Google for "bfactor ptraj" a number of hits come up
from the reflector that already describe how to do this.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 15 2013 - 14:30:02 PDT
