AMBER Archive (2007)

Subject: AMBER: SASA per residue

From: Evan Kelly (ebkelly_at_ualberta.ca)
Date: Mon Oct 22 2007 - 11:59:26 CDT

Hi Everyone,

I have been performing some MD simulations using Amber9 on a single
small protein and I would like to compare solvent accessible surface
areas on a per residue basis. I have then have two questions about
this:

1) It looks like the mm_pbsa script can do this, by setting the
surface tension parameter to 1. Is this the best way to do what I
require?

2) I have successfully been able to use mm_pbsa to obtain the .out
files (but not the statistics files as the program crashes). I get
standard output (see below), but I don't know what each of the
columns of data mean. Can anyone explain what each of these means?

GB
MS
1
TDC 1 43.885 2.114 -61.540 -15.459 309.976
TDC 2 57.367 8.017 8.333 -56.414 280.735
TDC 3 35.703 3.611 -65.467 -19.124 166.966
TDC 4 20.302 -2.138 0.029 -4.762 305.296
TDC 5 21.488 -0.486 -51.212 -7.065 78.043
TDC 6 22.462 0.230 4.340 -110.791 160.672
TDC 7 19.558 -0.594 14.158 -114.879 153.821
TDC 8 20.870 -2.582 -80.663 -7.814 123.665
TDC 9 15.250 -1.442 -16.673 -0.296 220.002
TDC 10 11.124 -1.110 -11.462 -1.228 56.606
TDC 11 43.601 0.263 21.510 -117.883 225.971
TDC 12 20.670 0.318 -6.105 -1.919 601.597
TDC 13 37.414 -0.380 -22.873 -0.244 573.450
TDC 14 17.790 -0.198 27.354 -116.044 400.807
SDC 1 21.148 0.481 -37.049 -12.944 260.567
SDC 2 33.181 5.449 4.981 -48.905 217.378
SDC 3 14.005 2.596 -55.174 -12.566 146.818
SDC 4 8.151 -1.337 -2.428 1.457 283.734
SDC 5 6.604 -2.248 -23.013 -0.934 71.030
SDC 6 8.353 1.812 13.133 -96.051 146.745
SDC 7 8.507 0.518 16.649 -98.779 139.825
SDC 8 10.520 -1.546 -65.759 -2.241 121.432
SDC 9 4.959 -1.620 -4.882 5.020 186.406
SDC 10 1.338 -0.910 2.578 0.364 47.363
SDC 11 26.770 -0.845 24.031 -105.143 174.768
SDC 12 8.468 -0.072 1.236 0.328 426.152
SDC 13 27.349 0.073 -13.694 -4.449 395.386
SDC 14 9.493 -0.034 22.718 -104.855 174.060
BDC 1 22.738 1.633 -24.492 -2.515 49.409
BDC 2 24.186 2.569 3.352 -7.509 63.357
BDC 3 21.698 1.015 -10.293 -6.558 20.148
BDC 4 12.151 -0.801 2.458 -6.219 21.562
BDC 5 14.884 1.762 -28.199 -6.131 7.013
BDC 6 14.109 -1.581 -8.793 -14.740 13.927
...................................................

Thanks!

----------------------------------
Evan Kelly
ebkelly_at_ualberta.ca

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