Hi,
You could try using cpptraj, which you may find simpler as it can
automate selection of hydrogen bond donors/acceptors. Note that in
cpptraj a hydrogen bond donor is defined as the heavy atom bonded to
the hydrogen, which is opposite ptraj.
You could try e.g.:
hbond acceptormask :PTR out numhbond.dat avgout hbavg.dat
See the Amber 15 manual for more details.
-Dan
On Thu, Apr 14, 2016 at 8:55 PM, Wu Xu <wxx6941.louisiana.edu> wrote:
> Dear Amber users and developers,
>
> I want to analyze h bond which phosphotyrosine (nonstandard amino acid) phosphate oxygen is involved using ptraj. I included the following in the input file (attached)
>
>
> donor mask :PTR.OP1
>
> donor mask :PTR.OP2
>
> donor mask :PTR.OP3
>
>
>
> The output file (attached as well) gave me the following error
>
> PTRAJ: donor mask :PTR.OP1
>
>
> Mask [:PTR.OP1] represents 0 atoms !!!NO ATOMS DETECTED!!!
>
> WARNING in ptraj, donor: No atoms selected (:PTR.OP1), ignoring...
>
> PTRAJ: donor mask :PTR.OP2
>
> Mask [:PTR.OP2] represents 0 atoms !!!NO ATOMS DETECTED!!!
>
> WARNING in ptraj, donor: No atoms selected (:PTR.OP2), ignoring...
>
> PTRAJ: donor mask :PTR.OP3
>
> Mask [:PTR.OP3] represents 0 atoms !!!NO ATOMS DETECTED!!!
>
> WARNING in ptraj, donor: No atoms selected (:PTR.OP3), ignoring...
>
>
>
> Your suggestions will be much appreciated.
>
>
>
> Thanks,
>
>
>
> Wu Xu
>
>
>
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> 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)
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Received on Fri Apr 15 2016 - 09:00:03 PDT
