Hi,
The 'hbond' command has been in cpptraj for a long time and is
relatively mature code. I've just done a quick test using the
following input and some of the files from the cpptraj test directory:
parm ../DPDP.parm7
trajin ../DPDP.nc
hbond HB donormask :12.N acceptormask :19.O avgout avghb.dat
distance d_N_O :12.N :19.O out nhb.dat
angle a_N_H_O :12.N :12.H :19.O out nhb.dat
The output in avghb.dat is this:
#Acceptor DonorH Donor Frames Frac
AvgDist AvgAng
ILE_19.O THR_12.H THR_12.N 69 0.6900
2.8626 160.5248
If I run the following awk command which calculate the hydrogen bond
as present when the distance is less than 3 and the angle greater than
135:
awk 'BEGIN{N=0;}{if ($2 < 3.0 && $3 > 135.0) N++;}END{print N;}' nhb.dat
the output is:
69
So in this case the 'hbond' command is working as it should. I tested
this with version 14.25 and the latest version (16.14). Please double
check your calculations. If you still believe there is a problem
please send me your complete cpptraj input and output, along with the
distance and angle data files. Thanks,
-Dan
On Thu, Sep 29, 2016 at 2:03 AM, Praneeth Bommisetti
<iampraneeth11.gmail.com> wrote:
> Hello all,
>
> I am trying to calculate the h-bond life time using the h-bond command
> in cpptraj of Amber 14.
>
> Command I used
>
> *hbond out hbd2l.out donormask :2-22 acceptormask :1&!.H avgout hbd2l.dat
> series *
>
> Output looked something like this
>
>
> #Acceptor DonorH Donor Frames Frac
> AvgDist AvgAng
> MOL_1.O3 DG5_2.HO5' DG5_2.O5' 30506 0.6101
> 2.7374 160.0488
> MOL_1.O1 DC_11.H42 DC_11.N4 22038 0.4408
> 2.8489 160.2850
> MOL_1.O1 DC_11.H41 DC_11.N4 7040 0.1408
> 2.8204 157.7933
> MOL_1.N6 DG_13.H22 DG_13.N2 3242 0.0648
> 2.9357 154.6688
> .
> .
> .
>
> I assumed the fraction to be the life time. That means 0.61 implies 61% of
> total frames
>
> To verify this, alternatively I calculated the distance between atoms and
> angles separately using cpptraj. Then, using excel, I made an adjoint set
> where the dist<3.0 and angle>135 which are defaults. But then the
> percentage of frames that satisfy these conditions exceeded significantly
> compared to the fraction given by cpptraj. Also the average angle and avg
> distance didn't match.
>
> Any idea on how these disparities are coming ?
>
> Any help would be appreciated.
>
> Thanks
>
> --
> *Regards, *
> *Praneeth Bommisetti, *
> *Fourth year Undergraduate,*
> *Integrated M.Sc Chemistry, *
> *Indian Institute of Technology Bombay.*
> *T: +918424815358, id:praneeth.b.iitb.ac.in <id%3Apraneeth.b.iitb.ac.in>*
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Sep 29 2016 - 06:30:03 PDT
