Hi,
On Mon, Jul 14, 2014 at 9:49 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> That said, I highly suggest that you upgrade to AmberTools 14 and switch to
> using cpptraj instead. The hbond command has been drastically simplified.
>
I second this. Your entire PTRAJ script could be one command in CPPTRAJ,
e.g.:
hbond H1 donormask :1-64.O= acceptormask :1-64.O= nointramol \
solventdonor :WAT solventacceptor :WAT.O \
out numhb.dat avgout avghb.dat solvout avgsolvent.dat bridgeout bridge.dat
I definitely recommend reading the manual to get an idea for what keywords
are available for the hbond command in CPPTRAJ and what they do. Good luck,
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
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 Jul 14 2014 - 09:30:02 PDT
