Hi,
On Sat, Oct 17, 2015 at 8:06 AM, Hadeer ELHabashy
<hadeer.elhabashi.gmail.com> wrote:
> and every time i got such errors
>
> Error: 'donor' is deprecated.
> Hydrogen bond acceptors and donors are defined within the 'hbond' action.
You are using ptraj syntax for 'hbond'. As noted in the manual,
'hbond' in cpptraj is one of the few commands not backwards-compatible
with ptraj. I highly recommend you read the Amber15 manual entry for
cpptraj 'hbond', section 29.9.25.
> I will probably specify in the trajin line the keyword 'binpos' that
> corresponds to the type of trajectory you are using, because I think that
> ptraj understand by default the traditional mdcrd files.
Actually, cpptraj (as with ptraj before it) autodetects the format of
input trajectories - you can name them whatever you want, and as long
as they are in a format supported by cpptraj they will be read in
correctly (binpos is one of these formats). A list of all 15
trajectory file formats currently read/written by cpptraj (along with
some helpful notes) are given in the Amber15 manual, Table 29.3 (page
540).
Hope this helps,
-Dan
--
-------------------------
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 Sat Oct 17 2015 - 08:00:04 PDT
