Hi,
On Thu, Sep 19, 2013 at 12:22 AM, Sumra Wajid Abbasi 30-FBAS/MSBI/F09
<sumra.msbi30.iiu.edu.pk> wrote:
> PTRAJ: donor mask :249.O4
> Mask [:249.O4] represents 0 atoms !!!NO ATOMS DETECTED!!!
> WARNING in ptraj, donor: No atoms selected (:249.O4), ignoring...
>
> PTRAJ: acceptor mask :374.N :198.H18
> Mask [:374.N] represents 0 atoms !!!NO ATOMS DETECTED!!!
> Mask [:198.H18] represents 0 atoms !!!NO ATOMS DETECTED!!!
> WARNING in ptraj, acceptor: No heavy atom was selected (:374.N), ignoring...
> WARNING in ptraj, acceptor: No hydrogen atom was selected (:198.H18),
> ignoring...
First, it's odd that you are specifying atoms as donors/acceptors that
don't exist in your system. Are you sure there should be hydrogen
bonds between the atoms you're defining? Also, you're using both an
angle and distance cutoff, so even if the atoms are close they will
not be recorded as hydrogen bonds if the angle isn't right.
You could try the 'hbond' command in cpptraj as well which takes some
of the guesswork out of specifying donors/acceptors.
-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) 585-9119 (Fax)
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Received on Thu Sep 19 2013 - 07:30:02 PDT
