Hi,
It's always useful to check your output for errors and warnings. In
your case the relevant message is at the end:
WARNING in ptraj(): No input trajectories specified (trajin), aborting...
You need to specify your combined trajectory with a 'trajin' command.
Also, I notice a lot of messages like this in your output:
WARNING in ptraj, acceptor: No heavy atom was selected (:HIP.ND1,NE2),
ignoring...
You may want to try using the 'hbond' command from cpptraj instead,
which is a little easier to set up (in my opinion at least).
Hope this helps,
-Dan
On Mon, Feb 16, 2015 at 7:29 AM, Ayesha Fatima
<ayeshafatima.69.gmail.com> 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
> 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 - 08:30:02 PST
