Dear Dr.Daniel and Dr. Jason
As far as I know, *'divergence'* is the newly introduced command of
the *program
cpptraj* in the *ambertool14*.
*What I want is:*
to use the command 'divergence' to find kullback-liebler divergence
between two data sets 'phi_sample1.dat' and 'phi_sample2.dat' where '
phi_sample1.dat' is a text file with 5000 phi dihedral angles in a column(I
mean, one angle in each line of the text file) and ' phi_sample2.dat' is
also a text file with 5000 phi angles in a column. These files were
generated by using dihedral command in cpptraj. The format of the file is
like
70.0
80.0
82.3
......
*What is given in the ambertool14 manual,28.12.6. divergence [page:552]:*
divergence ds1 <ds1> ds2 <ds2>
Calculate Kullback-Liebler divergence between specified data sets
*What command I used:*
cpptraj -i input_file -p topology_file
OR (In the interactive mode)
cpptraj
> divergence ds1 phi_sample1.dat ds2 phi_sample2.dat
*What error message I got:*
Error: Data set ds1 not found.
Error: Could not setup analysis [divergence]
Hope, these might be helpful in clearing the issue.
Thank you for help,
Mahendra Thapa
On Fri, Apr 18, 2014 at 4:09 PM, Thapa, Mahendra (thapamb) <
thapamb.mail.uc.edu> wrote:
>
>
>
> ________________________________________
> From: Daniel Roe
> Sent: Friday, April 18, 2014 2:05:56 PM (UTC-06:00) Central America
> To: AMBER Mailing List
> Subject: Re: [AMBER] How to use "divergence" command
>
> Hi,
>
> You need to post at least your entire cpptraj input (and ideally the
> output), as well as the version of cpptraj you are trying to use
> before we can help. I suspect there may be some warnings prior to the
> error message which may be useful in diagnosing your problem.
>
> -Dan
>
> On Fri, Apr 18, 2014 at 10:53 AM, Mahendra B Thapa <thapamb.mail.uc.edu>
> wrote:
> > Dear Amber users
> >
> > I tried to use the command "divergence" as given in ambertool14:
> > divergence ds1 <ds1> ds2 <ds2>
> >
> > But, I am getting the message as:
> > Error: Could not setup analysis [divergence]
> >
> > Please help me in this issue. I did a couple of trials with different
> data
> > sets, but no luck.
> >
> > Thank you for help
> > Mahendra Thapa
> > University of Cincinnati,OH
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Apr 21 2014 - 07:30:02 PDT
