Re: [AMBER] Query for Hbond lifetime analysis with AmberTools14

From: Daniel Roe <>
Date: Wed, 10 Sep 2014 07:52:37 -0600


You can specify a data set name to 'hbond' as with most other action
commands. Although in the manual the [<name>] option is missing, this
is just a typo - it is actually there. You then need to use the
'series' keyword so that cpptraj will track each individual hbond vs
time. The two relevant data set aspects (as listed in the manual) are
[solutehb] and [solventhb]. So if you wanted to calculate
solute-solute hydrogen bond lifetimes you could use something like the

parm <topology>
trajin <trajectory>
# Look at protein backbone hydrogen bonds only, data set name H1
hbond H1 series .N,H,C,O
runanalysis lifetime H1[solutehb] out life.dat

See the manual for full details on the 'hbond' and 'lifetime' commands.


On Wed, Sep 10, 2014 at 4:00 AM, Indrajit Deb <> wrote:
> Dear AMBER users,
> I have queries regarding the hbond analysis command using cpptraj with
> AmberTools14.
> I found in the mailing list that it has been suggested to use run command
> after hbond command followed by runanalysis command to calculate the hbond
> lifetime. But those instructions were for AmberTools13. In AmberTools13, in
> case of hond analysis with cpptraj there was an option as follows:
> "hbond [<dataset name>]"
> this data can be used for lifetime analysis.
> But in case of AmberTools14, there is no "[<dataset name>]" option, then
> how to calculate the lifetime.
> Please suggest
> -----indrajit
> ---------------------------------------------------------------------
> Indrajit Deb
> Kolkata, India.
> Mob: +919239202278
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Sep 10 2014 - 07:00:04 PDT
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