Re: [AMBER] ptraj binary missing from AmberTools 13 install?

From: Daniel Roe <>
Date: Wed, 23 Jul 2014 14:42:48 -0600


Yes, ptraj has been retired as of AmberTools 14. Almost all ptraj scripts
should be backwards compatible with cpptraj, although there are a few
exceptions (e.g. 'hbond'). If you try cpptraj with your scripts and find
they do not work, you can manually build ptraj by going into the ptraj
source directory (assuming you have already configured and built
AmberTools) and typing 'make install' from there, e.g.

cd $AMBERHOME/AmberTools/src/ptraj
make install

Hope this helps,


PS - If you try cpptraj and find it doesn't work, if you could let me know
what didn't work (either via direct email or over the list) I'd appreciate
it. Since ptraj is no longer being actively developed it's best if users
can seamlessly transition to cpptraj...thanks!

On Wed, Jul 23, 2014 at 2:14 PM, Raik Grünberg <>

> Hi,
> this sounds like a silly question (to me at least) but I just compiled
> / installed AmberTools 13 and there doesn't seem to be any ptraj
> binary anywhere. cpptraj is there but I have a large body of ptraj
> input scripts wrapped by python code and wouldn't want to convert all
> of it. Has ptraj been discontinued? There is no ptraj section in the
> manual any longer but on the other hand it is mentioned everywhere
> including on the main AmberTools web site.
> Many thanks in advance,
> Best regards,
> Raik
> --
> ___________________________________
> Raik Grünberg
> ___________________________________
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
AMBER mailing list
Received on Wed Jul 23 2014 - 14:00:02 PDT
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