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
>> > _______________________________________________
>> > 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 - 10:30:04 PST
