Well, it's a pitty a didn't "triple check" then I would notice that you
set distance cutoff in cpptraj with "dist" not "cut" like in ptraj.
Sorry for wasting your time.
> Hi,
> I double checked to be sure I've done it correctly and it seems that the
> big differences in hbond occurance calculated by ptraj and cpptraj are
> present despite the exact same settings of the distance and angle cutoffs
> (3.2 and 120, respectively).
>
> Regards,
> Piotr Maj
>
>
>> 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
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> 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)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jun 03 2013 - 05:30:03 PDT
