Ok. Thanks. Now it says that I have to specify a window size. I guess that
the answer to this question may vary from system to system, but, is there a
"consensual" window size?
2013/10/30 Daniel Roe <daniel.r.roe.gmail.com>
> Hi,
>
> On Wed, Oct 30, 2013 at 2:02 PM, Fabrício Bracht <fabracht1.gmail.com>
> 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 ...
> run
> runanalysis lifetime out solute.lifetime.dat bond1[solutehb]
>
> Hope this helps,
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Wed Oct 30 2013 - 13:30:04 PDT
