AMBER Archive (2005)

Subject: AMBER: Some explanations of MM_PBSA @DECOMP OUTPUT file?

From: Peng Tao (amberhelp_at_gmail.com)
Date: Thu Dec 01 2005 - 10:35:09 CST

Dear All,

In the MM_PBSA example came with AMBER8, some output files are not explained
very clearly by the manual. Could you please help me to understand the
following output files?

1)
 $AMBERHOME/amber8/src/mm_pbsa/Examples/05_MMPBSA_Decomp_Residue/ras_raf_II_wt_statistics.out.save

I cut the part of the file here, since each line is very long.
/////////////////////////////////////////////////////////////////////////////////////
=>> COMPLEX

Number Residue SINT BINT ...

0 35 3.08 *0.91* 6.83 *1.39*
     ...

1 36 9.81 *0.84* 10.00 *1.06*
...

2 37 7.80 *3.28* 9.48 * 1.21*
...

...

/////////////////////////////////////////////////////////////////////////////////////

I know the meaning of SINT, BINT, etc. But what is the number after each
column of energies? For example, 3.08 is the SINT(Sidechain bond, angle,
dihedral energies according to AMBER manual), so what is 0.91? My guess is
that 0.91 might be the standard error of SINT energy, since SINT energy is
calculated based on several snapshots. But I cannot confirm it.

2) In another output file:

$AMBERHOME/amber8/src/mm_pbsa/Examples/05_MMPBSA_Decomp_Residue/ras_raf_II_wt_com.all.out.save

/////////////////////////////////////////////////////////////////////////////////////

MM
GB
MS
1
TDC 35 11.517 -0.209 -15.651 -3.441 547.811
TDC 36 18.067 -0.868 -5.819 -4.616 373.041
TDC 37 14.012 -2.445 -35.637 -28.937 200.836
TDC 38 10.848 -1.976 -26.426 -37.854 276.224

......
/////////////////////////////////////////////////////////////////////////////////////

What is the meaning of last five columns (11.517 -0.209 -15.651 -
3.441 547.811)?

Thanks a lot in advance.

Best Regards,
Peng Tao

The Ohio State University

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