Hi,
You'll need to add the 'series' keyword of the 'hbond' command to
ensure the hydrogen bond time series data is saved, then use the
'lifetime' analysis command on that time series data. One thing to be
mindful of is that since the 'hbond' command does not know a priori
what hydrogen bonds will be present you need to actually generate the
time series data before running the analysis. For example, this input
will perform lifetime analysis on solvent-solute backbone hydrogen
bonds:
hbond H1 series .N,H,C,O solventdonor :WAT solventacceptor :WAT.O
run
runanalysis lifetime H1[solventhb] out solventhb.lifetime.dat
See the manual for full details of both commands and more examples.
-Dan
On Fri, Aug 3, 2018 at 9:01 AM, ATUL KUMAR <atul44_sit.jnu.ac.in> wrote:
> Dear Amber Users,
> I want to calculate the solute-solvent hydrogen bond lifetime using
> hbond command of cpptraj. Can anyone point me in the right direction?
> Any help will be appreciated.
> Thank you.
>
>
> *Atul Kumar Jaiswal*
> Research Scholar
> School of Computational and Integrative Sciences
> Centre for Computational Biology and Bioinformatics (CCBB)
> JNU, New Delhi
> India.
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Received on Mon Aug 06 2018 - 06:30:02 PDT
