Hi
On Sunday, February 22, 2015, Ayesha Fatima <ayeshafatima.69.gmail.com>
wrote:
> Dear all,
> I have run the hbond analysis in cpptraj using AmberTools 13. As
> specified in the manual of Amber14, the input
If you are using syntax from the Amber14 manual, you should use cpptraj
from Amber14/AmberTools14.
-Dan
> syntax for lifetime
> analysis should be something like this
>
> lifetime [out <filename>] <dsetarg0> [ <dsetarg1> ... ] [window
> <windowsize> [name <setname>]] [averageonly] [cumulative] [cut
> <cutoff>] [greater | less]
>
> Using this cue and from the amber mailing lists suggestions I wrote the
> input as
> runanalysis lifetime H1[solutehb] out life.dat
>
> In the reference manual it states:
> [window <windowsize>] Size of window (in frames) over which to
> calculate lifetimes/averages. If not specified lifetime/average will
> be calculated over all sets
>
> This understandable and I did not specify the window. My run
> terminates in Error: Output file name specified but no window size
> given ('window <N>')
>
> If I specify the window size there is no error and I generate the
> three files. the data in the files looks like this
> #Frame LYS_211. LYS_211. LYS_211. LYS_211. LYS_211. TRP_249. TRP_249.
> TRP_249.
> 1 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
>
> >From an earlier mail I received from Daniel, If the window is not
> specified the output should look like this
>
> #Set Nlifetimes MaxLT AvgLT TotFrames SetName
> 0 19 4 1.4211 27 GLU_13.O-VAL_2.N-H
>
> Despite repeated efforts I am unable to get this output as when I dont
> write the window size, the run terminates. Is there another keyword to
> be added somewhere? Please share your experience, I am sure, I am not
> doing something correct. My input without window looks like this
> ............................
> trajin combined1-25.nc
> hbond H1 series donormask
> :178,211,249,251,252,253,281,
> 542,543,544,545,546,547.N*,H*,C*,O*
> acceptormask :568.0 \
> out hb5.dat dist 3.5 avgout avg5.dat
> run
> writedata solute.dat H1[solutehb]
> runanalysis lifetime H1[solutehb] out life.5.dat
> ....................
>
> Thank you once again to Daniel and others for being very helpful.
>
> Regards
> Ayesha Fatima
>
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>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
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 Sun Feb 22 2015 - 08:00:02 PST
