Hi All,
I used idecomp=1 during sander minimization in amber7 with igb=2
but I get an ouput where the energy(ies) occasionally drops
to zero and eventually stays at zero after a particular residue
(around residue 340, a lysine):
...
SDC 325 -5416.339 -291.059 2290.886 386.871 17645.748
SDC 326 5348.581 -1703.869 -2649.635 1671.587 12751.497
SDC 327 0.000 0.000 0.000 0.000 *********
SDC 328 ********* -396.839 -314.581 ********* 17942.770
SDC 329 0.000 0.000 0.000 0.000 *********
SDC 330 -6590.715 -451.888 -124.687 -769.142 -5944.257
SDC 331 -5037.502 -699.177 -337.564 80.948 24777.773
SDC 332 -5943.068 -625.720 2568.128 -117.873 13649.542
SDC 333 -2958.929 -518.837 4352.322 837.015 16908.693
SDC 334 -1853.662 -606.598 1773.567 -9.420 21299.693
SDC 335 -2373.974 -247.162 -3281.783 -617.270 -2204.613
SDC 336 -1249.443 -130.762 3455.217 1514.927 13183.664
SDC 337 815.730 -156.432 252.705 -94.055 7444.072
SDC 338 -777.803 -136.057 -3544.832 -2250.628 1616.855
SDC 339 -1958.231 -2.409 -111.460 -1862.751 -3658.351
SDC 340 443.122 -414.384 -6613.113 -3566.652 10035.924
SDC 341 0.000 0.000 0.000 0.000 -642.089
SDC 342 0.000 -146.137 262.610 -461.576 2210.714
SDC 343 0.000 -236.619 -4037.192 -1597.852 -1464.845
SDC 344 0.000 -158.396 1074.980 -112.323 -8506.592...
(All internal energies = 0.000 until the end of this section
of the output - similarly for TDC and BDC sections.)
Does anybody have an idea what this means or what I might be
doing wrong? Below is my min.in file.
minimization run:
&cntrl
imin=1,
maxcyc=200,
ntpr=1,
ntf=1,
ntb=0,
idecomp=1,
igb=2,
gbsa=1,
offset=0,
surften=1.0
dielc=1,
extdiel = 80.0,
saltcon = 0.15,
cut=10000.0,
nsnb=10000,
scnb=2.0,
scee=1.2,
&end
Simple Energy Minimization with GB
RES 1 625
END
END
Thanks you,
Mark
Received on Wed Oct 30 2002 - 10:11:02 PST
