Relating to Dan's example,
I think one should add "netcdf" keyword along trajout command
trajin t1.nc
trajin t2.nc
trajin t3.nc
strip :WAT outprefix strip
autoimage
trajout combined.nc netcdf <
http://combined.nc>
regards
Vijay
On Tue, Feb 17, 2015 at 1:00 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> On Monday, February 16, 2015, Mahmood Jasim <ddfd09.gmail.com> wrote:
> >
> > I think you need to do the centering and stripping on the individual
> > trajectories first and then combine the centered and stripped
> trajectories.
>
>
> Actually you can do stripping, centering etc in one run. For example
> (cpptraj syntax):
>
> trajin t1.nc
> trajin t2.nc
> trajin t3.nc
> strip :WAT outprefix strip
> autoimage
> trajout combined.nc
>
> -Dan
>
>
> >
> > Also try to open the combined trajectory in VMD just to make sure that
> you
> > are actually getting a trajectory file
> >
> > Regards
> > Mahmood
> >
> > On 16 February 2015 at 14:29, Ayesha Fatima <ayeshafatima.69.gmail.com
> > <javascript:;>>
> > wrote:
> >
> > > Dear all,
> > > I am trying to combine my trajectoriesto reduce the memory requirements
> > of
> > > ptraj to run the hbond anlaysis facility. there is no error in making
> the
> > > combined trajectory, however when i run the hbond analysis, the
> > > trajectories are not read. Any advise is useful. I am using Amber 12.
> > > Thank you
> > > Ayesha Fatima
> > > PhD candidate UM
> > >
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> > >
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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 Feb 16 2015 - 21:30:02 PST
