Dear Ambers,
I am trying to run NMODE for RNA. SANDER is used to carry out
conjugate gradient minimization. Due to the large electrostatic
repulsion force between two chains, I minize the RNA in implicit
solvent using GB option(igb=1), which outputs an energy item
called "EGB", and includes this energy in the total enegy calculation.
But in NMODE program, there is no GB option. EGB will not be included
so that the good RMSD values gotten from minimization is lost. For
example,
in minimization:
NSTEP ENERGY RMS GMAX NAME NUMBER
334 -1.6941E+04 9.5323E-06 5.3453E-05 O1P 879
BOND = 131.3735 ANGLE = 429.9608 DIHED = 1602.1850
VDWAALS = -1472.6783 EEL = 31155.2120 EGB = -40579.6742
1-4 VDW = 551.7269 1-4 EEL = -8758.9700 RESTRAINT = 0.0000
but in nmode:
step = 0
F = 0.236388E+05 GRDMAX = 0.430208E+02 GNORM = 0.678876E+01
E-NONB E-ELE E-HBOND E-BOND
-0.14727E+04 0.31155E+05 0.00000E+00 0.13137E+03
E-ANGLE E-DIHED E-NB14 E-EEL14
0.42996E+03 0.16022E+04 0.55173E+03 -0.87590E+04
E-POL E-3BOD
0.00000E+00 0.00000E+00
Root-mean-square gradient of input coords is 6.78876393
This is greater than the requested maximum: 1.E-05
Using explicit solvent may be able to fix this probelm(I am not sure
if NMODE will include EAMBER or not), but much more expensive. Does
anybody have other suggestions? Thank you so much!!
All the best
Shawn Hu
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Received on Sun May 30 2004 - 23:53:00 PDT
