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
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Received on Thu Feb 05 2015 - 11:00:03 PST
