AMBER Archive (2004)

Subject: AMBER: question about NMODE for RNA

From: xhu1_at_memphis.edu
Date: Sun May 30 2004 - 17:32:22 CDT


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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