Hi,
As stated in the manual, the 'hbond' command in cpptraj is one that
has changed quite a bit from the way it was implemented in ptraj. For
one, in ptraj the default value for the angle cutoff is 120.0 (note
this is different than what the manual states; this should be
corrected in the manual) whereas in cpptraj the default is 135.0.
Also, as you noted in ptraj hbond output angles are reported as
deviations from linear whereas in cpptraj the actual angle value is
reported. If you explicitly set the distance and angle cutoffs the
results should then match (within round-off).
Hope this helps,
-Dan
On Fri, May 31, 2013 at 7:14 AM, <pmaj.nencki.gov.pl> wrote:
> Dear all,
> I am surprised by different results obtained with hbond command in ptraj
> and cpptraj. For the same dataset both programs calculated different
> parameters of hydrogen bonds, for example:
> in ptraj:
> | 3265 :205.OD1 | 9201 :579.H3 9183 :579.N3 | 85.41 2.973 ( 0.12)
> 19.14 ( 9.59) 7.6 ( 11.3) 123
> in cpptraj:
> ASN_205.OD1 UMP_579.H3 UMP_579.N3 3935 0.4919
> 2.8892 161.4452
> So besides small differences in the average distance and angle (I know
> that in ptraj 19.14 degrees means 180-19.14=160.86) of the bond, there are
> big differences in the fraction of frames the bond is present (in the
> example 85.41% vs 49.19%). It's similar for all other bonds.
> What might be causing such differences and which results can be considered
> "correct"?
>
> Regards,
> Piotr Maj
>
>
>
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--
-------------------------
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 Fri May 31 2013 - 07:30:03 PDT
