Hi,
On Monday, February 16, 2015, Vijay Achari <glycoamber.gmail.com> wrote:
> Relating to Dan's example,
>
> I think one should add "netcdf" keyword along trajout command
You dont need to with cpptraj. It knows that the '.nc' extension means
netcdf. Same thing for .pdb, .mol2, etc.
-Dan
>
> 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
> <javascript:;>> wrote:
>
> > On Monday, February 16, 2015, Mahmood Jasim <ddfd09.gmail.com
> <javascript:;>> 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:;>
> > > <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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> >
> >
> > --
> > -------------------------
> > 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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> >
> _______________________________________________
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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 Tue Feb 17 2015 - 01:00:02 PST
