Hello
It is also strange for me why i am receiving such warnings. As in input
file i have defined only those atoms as donors/acceptors which were
observed to be involved in hydrogen bond interactions at every ns using VMD.
Regards
Sumra Wajid Abbasi
PhD Scholar
Computational Biology Lab, National Center for Bioinformatics
Quaid-e-Azam University, Islamabad-45320 Pakistan.
On Thu, Sep 19, 2013 at 7:15 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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 - 07:30:03 PDT
