yes, exactly. But I want to measure hydrogen bonding between proton
and acceptor using cpptraj
Niko
Quoting Maciej Maciejczyk <maciej.maciejczyk.uwm.edu.pl>:
> I think that cpptraj returns distance between heavy atoms and you
> probably measure distance between proton and acceptor in VMD
>
> MM
>
>
> On 20.02.2019 10:36, Niko Prasetyo wrote:
>> dear all,
>>
>>
>> I did a hbond analysis for two fragment, caffeine and metacrylic acid
>> using cpptraj..
>>
>> here the command that I used
>>
>>
>> hbond hbond_test out hbond angle 30.0 dist 3.0 donormask :met.O1
>> donorhmask :met.H5 acceptormask :aff.O1 avgout aaa nointramol series
>> uuseries bbb
>>
>> from the hbond analysis, the distance is about 2,7 angstroem and the
>> angle is 159 degree..
>>
>> I simply check the distance between these two fragment via VMD, and
>> the average is should be 1.8 angstroem...
>>
>> my question is why the hbond distance from cpptraj is much longer?
>>
>> thank you in advance for the answers,
>>
>> Best
>>
>> Niko
>>
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>
> --
> *******************************************
> Maciej S. Maciejczyk, PhD
> Division of Physics and Biophysics
> Faculty of Food Sciences
> University of Warmia and Mazury in Olsztyn
> ul. Oczapowskiego 4
> 10-719 Olsztyn
> Poland
> *******************************************
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Received on Wed Feb 20 2019 - 03:00:03 PST
