Dear Amber users
I have taken an NMR structure of a small protein and minimized it with
sander in implicit solvent (igb=1). My output is as follows:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -3.6789E+02 1.7668E+01 1.8766E+02 O 334
BOND = 65.9631 ANGLE = 61.8355 DIHED =
298.1987
VDWAALS = 44.4613 EEL = -2385.5904 EGB =
-739.8229
1-4 VDW = 198.2850 1-4 EEL = 2088.7822 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1000 -8.8062E+02 7.4882E-02 5.1163E-01 C 529
BOND = 18.6956 ANGLE = 61.2032 DIHED =
256.7138
VDWAALS = -223.5801 EEL = -2398.7351 EGB =
-729.0717
1-4 VDW = 101.0093 1-4 EEL = 2033.1486 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
2000 -8.9380E+02 1.0086E-01 6.8560E-01 CE1 393
BOND = 18.8494 ANGLE = 61.0641 DIHED =
252.0533
VDWAALS = -228.2521 EEL = -2407.6584 EGB =
-728.9162
1-4 VDW = 102.8656 1-4 EEL = 2036.1992 RESTRAINT =
0.0000
etc etc with increasing energy, which then eventually begins to decrease
again.
Does anyone out there know why I have such a drastic energy increase when I
only expect ever to see a decrease?
My sander input file is:
minimization with sander (Amber9)
&cntrl
imin = 1, maxcyc = 50000, drms = 0.005, ntb = 0,
ntpr = 1000, cut = 80., igb = 1, rgbmax = 40, ncyc = 100
&end
Many thanks in advance
Hayden Eastwood
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Received on Sun May 27 2007 - 06:07:11 PDT
