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
>>
>>
>>
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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 Mon Jun 03 2013 - 03:30:02 PDT
