On Mon, Sep 8, 2014 at 2:45 AM, James Starlight <jmsstarlight.gmail.com> wrote:
> 1) need to remove periodicity and wrapping from my trajectory
>
> trajin md.nc 1000 last 5
> reference protein.inpcrd
> unwrap
> center :1-289 mass origin
> image origin center
This is not a useful command sequence and the exact opposite of what
you want. You are unwrapping (i.e. removing imaging) and then
re-imaging. If you want to remove wrapping just use 'unwrap'. I
strongly recommend you read the manual and become familiar with every
command you try to use before you run your calculations.
> 2) if I chose possibility to save trajectory after RMSD fitting
> trajin md.nc 1000 last 5
> reference protein.inpcrd
> rms reference :1-289.CA out rmsd.dat
> outtraj afterRMSD.nc
>
> it has produced correct RMSD.dat output but no any processed trajectory
> afterRMSD.nc has been appeared in the work dir.
If you have multiple topologies specified cpptraj will try to use the
first topology for 'trajout'/'outtraj' commands, and if that topology
does not match the topology for the input trajectory the output
trajectory will not be written. However, without seeing your complete
cpptraj output I can only speculate.
-Dan
>
> Thanks for help,
>
> James
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
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Received on Mon Sep 08 2014 - 07:00:08 PDT
