AMBER Archive (2006)

Subject: AMBER: Again SASA

From: lucas luquitas (lucamaster_at_gmail.com)
Date: Mon May 22 2006 - 14:51:22 CDT

Hi, I am resending a mail I posted some time ago,

I am trying to calculate SASA for every step of a trajectory for every
aminoacid.
I understand that it can be done with mm_pbsa.pl program.
But when I see the output(snapshot__at_.all.out) I do not understand it,
it seems logical that the last column is related to SASA, but I would like to
understand what is in the output at every column. I could not find
this information
in the Amber manual.

Thanks,

Lucas

MM
GB
MS
1
TDC 1 8.549 0.107 -90.555 5.106 109.741
TDC 2 13.047 1.148 8.274 -6.235 104.062
TDC 3 15.467 -1.023 5.614 -5.461 55.973
TDC 4 24.623 -1.478 -12.526 -2.157 80.165
...............
SDC 1 4.240 0.512 -69.100 10.325 103.891
SDC 2 3.129 -0.320 3.410 -0.250 74.105
SDC 3 1.337 -0.031 -9.012 5.716 31.281
SDC 4 11.477 -0.569 -6.353 5.844 78.514
.........
BDC 1 4.309 -0.405 -21.456 -5.219 5.850
BDC 2 9.917 1.468 4.863 -5.985 29.957
BDC 3 14.130 -0.992 14.626 -11.177 24.693
BDC 4 13.146 -0.909 -6.173 -8.001 1.651
BDC 5 11.267 -0.254 -8.449 -6.649 0.000
BDC 6 11.924 -1.312 -13.065 -4.373 23.261
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Lucas
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