Hi,
Was this system run with periodic boundary conditions? If that is the
case, since it seems you are calculating hydrogen bonds between two
molecules it is possible the discrepancy is due to imaging - by
default the 'distance' command performs imaging, while the 'hbond'
command does not. In this case I would recommend trying one or more of
the following:
1) Use the 'hbond' command with the 'image' keyword and see how your
results change. I highly recommend using cpptraj from AmberTools 16
for this since I think AT14 'hbond' only images distances, not angles,
while AT16 cpptraj does both.
2) Use 'autoimage' prior to the 'hbond' command.
I think 1) is your best bet. Let me know if this helps,
-Dan
PS - If this is indeed the issue then I need to consider turning
imaging on for 'hbond' by default...
On Thu, Sep 29, 2016 at 9:22 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
--
-------------------------
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 Wed Oct 12 2016 - 07:30:02 PDT
