Dear Dr. Danial
Thanks for help
I have checked cpptraj 'hbond', section 29.9.25. upon your recommendation
and I came up with this lines for cpptraj
trajin 2y3j_pc_md.crd
hbond out N_H1_OXT.out donormask :1.N donorhmask:1.H1 acceptormask :6.OXT
series hbt
what do you think may be wrong or missing in the second line ?!
Regards
Hadeer
On Sat, Oct 17, 2015 at 4:42 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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 - 08:30:03 PDT
