Hi Kenneth,
yes combination of AWK and CALC has been perfect for me! Thanks for
suggestions again!
James
2015-02-05 19:52 GMT+01:00 Kenneth Huang <kennethneltharion.gmail.com>:
> James,
>
> Like you mentioned in the other thread, I think you should be able to just
> look at the total energy in the final_decomp file, and just use that as a
> means of comparison of which residues are having more contribution across
> different ligands, etc.
>
> Regarding the your other question from the other thread-
>
>
> > Here the idea that I define some threshold and
> > scan all strings (Residues) from the final_decompos_output.dat file. So
> If
> > residue has total score (in fact I don't know here what value should I
> take
> > into account assuming that I make my output using verbose=0 option)
> higher
> > than this threshold - I copy the string to some new txt file called
> > decompose_top.txt. Eventually I repeat this in loop for each of my
> > output.dat files obtaining equal number of new output files for the same
> > systems with 10-15 top residues-contributors. Does this approach is good
> in
> > general or there are better alternatives to rank decomposition outputs?
>
>
> Other values you get from a more verbose output might be able to describe
> more information to you, depending on what you're looking for. In the range
> of what you're suggesting (rank residue contributions, then see which ones
> differ between different ligands to see which ones are distinguishing based
> on ligand characteristics?) I think you should be fine with just
> dec_verbose=0. Though, I'd usually do something like this in Excel, or a
> similarly based tool just for simplicity of being able to compare them side
> by side.
>
> Best,
>
> Kenneth
>
>
> On Tue, Feb 3, 2015 at 9:34 AM, James Starlight <jmsstarlight.gmail.com>
> wrote:
>
> > Dear Amber users!
> >
> >
> > What are the general idea might be here most useful? Will it possible
> to
> > rank top residues in case of each system within each of the decomposition
> > output log file?
> >
> > Thanks for any ideas,
> >
> > James
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Ask yourselves, all of you, what power would hell have if those imprisoned
> here could not dream of heaven?
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 06 2015 - 01:30:04 PST
