Hi,
On Monday, February 16, 2015, Ayesha Fatima <ayeshafatima.69.gmail.com>
wrote:
>
> Yet I am having the problem. However, this time i will try with cpptraj.
Ok, but be aware that 'hbond' syntax in cpptraj is different than ptraj, so
read the Amber 14 manual entry carefully.
> About opening in VMD, the combined trajectory is read as you would load a
> CRD with no periodic box file type.. I will try again and see what happens.
I recommend you use NetCDF files in the future to avoid potential box/no
box issues (and NetCDF files are just better in every way in my opinion).
-Dan
> Thank you again
>
> 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
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org <javascript:;> <javascript:;>
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org <javascript:;> <javascript:;>
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > --
> > -------------------------
> > 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)
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org <javascript:;>
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <javascript:;>
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 16 2015 - 11:00:03 PST
