Thank you for help i will definitely go for cpptraj
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 7:42 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Thu, Sep 19, 2013 at 8:28 AM, Sumra Wajid Abbasi 30-FBAS/MSBI/F09
> <sumra.msbi30.iiu.edu.pk> wrote:
> > 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.
>
> However according to your PTRAJ output, residue 249 does not contain
> an atom named O4:
>
> >> > PTRAJ: donor mask :249.O4
> >> > Mask [:249.O4] represents 0 atoms !!!NO ATOMS DETECTED!!!
> >> > WARNING in ptraj, donor: No atoms selected (:249.O4), ignoring...
>
> If you are identifying atoms by selecting them in VMD, be aware that
> the 'residue' field numbering starts from 0. When using Amber
> topologies in VMD it is better to use the 'resid' field, which starts
> from 1 (this is the convention all Amber programs follow).
>
> You can easily test the results of mask selection in cpptraj's
> interactive mode with the 'select' or 'parminfo' commands.
>
> Hope this helps,
>
> -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 - 08:00:04 PDT
