Re: [AMBER] Hbond analysis

From: Daniel Roe <>
Date: Wed, 30 Oct 2013 14:12:25 -0600


On Wed, Oct 30, 2013 at 2:02 PM, Fabrício Bracht <> wrote:
> I have one more question about lifetime analysis. I've tried
> hbond bond1 out nhb1.dat :1-342 dist 3 series donormask
> :204&!.CA,CB,C|:342.O acceptormask :204.OD1,OD2|:342.O avgout avghb1.dat
> solventdonor :WAT.O solventacceptor :WAT.O bridgeout bridge1.dat solvout
> solvent1.dat
> lifetime lifeout bond1
> But I get
> Error: lifetime: No data sets selected.
> Error: Could not setup analysis [lifetime]

This is actually related to how the 'hbond' action generates
time-series data. In most actions you know what data you will generate
beforehand; for example, with 'distance' you know you will have 1 data
set generated containing distances. This data set is created as soon
as cpptraj processes the 'distance' command, so any subsequent
actions/analyses know that it's there. With 'hbond series' however,
cpptraj doesn't know whether any hydrogen bonds will be formed or not,
so those data sets aren't created until you actually process your
trajectory frames. Therefore the [solutehb] and [solventhb] time
series data sets aren't created until you 'run'. The solution is to
add a 'run' command after hbond so that trajectory frames are
processed and hbond time series data is created, then run the lifetime
analysis by itself. For example, something like:

hbond bond1 ...
runanalysis lifetime out solute.lifetime.dat bond1[solutehb]

Hope this helps,


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Oct 30 2013 - 13:30:04 PDT
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