James,
I'm honestly not sure- you might be able to write a program to strip out
the extraneous sections, but I don't know of any other methods available.
If there is, someone else might be able to point you in the right
direction.
The only way I know how to consistently get dG as the last column is to
have it print decomposition for all the residues. Otherwise, the solution I
tend to use to just manually edit each entry one at a time into a new
formatted table, which I can imagine is a tedious endeavor the more
residues you print out.
Best,
Kenneth
On Fri, Feb 6, 2015 at 1:14 PM, James Starlight <jmsstarlight.gmail.com>
wrote:
> BTW is it possible to take out any error message from the decomposition
> data which looks like
> Residue | Location | Internal | van der Waals |
> Electrostatic | Polar Solvation | Non-Polar Solv. | TOTAL
>
> -------------------------------------------------------------------------------------------------------------------------------------------------------
> ASN 1 | R ASN 1 | 0.000 +/- 0.000 | -0.000 +/- 0.000 | 0.045
> +/- 0.034 | -0.045 +/- 0.034 | 0.000 +/- 0.000 | 0.000 +/-
> 0.001
>
> to obtain always dG in the last column ? It's necessary for my scripting
> :)
> Also it'd be good to obtain only 2 values: residue number and total dG as
> the output :)
>
> James
>
> 2015-02-06 10:07 GMT+01:00 James Starlight <jmsstarlight.gmail.com>:
>
> > 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
> >> > _______________________________________________
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> >> > 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?
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> >>
> >
> >
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Received on Fri Feb 06 2015 - 15:00:02 PST
