Re: [AMBER] Hydrogen bond analysis problem

From: Daniel Roe <>
Date: Thu, 19 Sep 2013 08:42:50 -0600


On Thu, Sep 19, 2013 at 8:28 AM, Sumra Wajid Abbasi 30-FBAS/MSBI/F09
<> 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,


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Thu Sep 19 2013 - 08:00:03 PDT
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