Hi Dan,
thank you very much for the help! Indeed in the second case the problem was
due to the topology
BTW I've triet to prepare topologies with no box and stripped from water
taking command sequence from the tutorial- but the resulted topology could
not recognized by VMD.
parm system.parmtop
parmstrip :WAT
parmbox nobox
parmwrite out stripped.parmtop
Where might be error?
James
2014-09-08 17:59 GMT+04:00 Daniel Roe <daniel.r.roe.gmail.com>:
> 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
> (801) 585-6208 (Fax)
>
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Received on Mon Sep 08 2014 - 23:30:02 PDT
