AMBER Archive (2006)

Subject: Re: AMBER: mm-pbsa output

From: alfredoq_at_fcq.unc.edu.ar
Date: Thu Sep 21 2006 - 06:29:51 CDT

Dear Stefano:
             Check the mm_pbsa tutorial
(http://amber.scripps.edu/tutorial/AMBER-MM_PBSA-tutorial_v8.pdf) in order to
find the meaning of each term in the output. In the final section of the
tutorial you will find Appendix B where the terms are indicated
Best wishes

Alfredo

Quoting Stefano Pieraccini <Stefano.Pieraccini_at_unimi.it>:

>
> Hi all,
>
> I'm using mm-pbsa in amber 9. I tried to decompose the interaction
> between two protein monomer in the pairwise mode. I obtained this
> output (see below), but I was not able to find anywhere what does
> each of the five columns of number represent. In the mailing list
> there is a lot about mm.pbsa, but not on this specifical subject.
> Does anyone know what is the exact meaning of these numbers?
>
> Thank you in advance
>
> Stefano Pieraccini
>
>
>
> MM
> GB
> MS
> 1
> TDC 1-> 1 0.000 1.443 -3.320 -76.176 608.033
> TDC 1-> 2 0.000 -0.174 22.488 -26.127 -186.432
> TDC 1-> 3 0.000 -0.327 -19.712 19.485 -19.563
> TDC 1-> 4 0.000 -0.015 -1.192 1.088 0.000
> TDC 1-> 5 0.000 -0.004 0.187 -0.193 0.000
> TDC 1-> 6 0.000 -0.001 -0.156 0.153 0.000
> TDC 1-> 7 0.000 0.000 0.042 -0.042 0.000
> TDC 1-> 8 0.000 0.000 0.171 -0.168 0.000
> TDC 1-> 861 0.000 0.000 -0.041 0.041 0.000
> TDC 1-> 862 0.000 0.000 -2.633 2.600 0.000
> TDC 1-> 863 0.000 0.000 -0.016 0.016 0.000
> TDC 1-> 864 0.000 0.000 -0.004 0.004 0.000
> TDC 1-> 865 0.000 0.000 -0.056 0.056 0.000
> TDC 1-> 866 0.000 0.000 0.004 -0.004 0.000
> TDC 1-> 867 0.000 0.000 0.026 -0.026 0.000
> TDC 1-> 868 0.000 0.000 -5.008 4.946 0.000
>

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Facultad de Ciencias QuĂmicas - Universidad Nacional de CĂrdoba

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