On Mon, Jul 15, 2013 at 2:23 PM, Parker de Waal <Parker.deWaal09.kzoo.edu>wrote:
> Hi Jason,
>
> 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.
> rms first 1-465.CA
>
You should use "reference" instead of "first", since you want to align to
the reference average structure instead of the first structure in your
trajectory.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jul 15 2013 - 14:00:03 PDT
