Dear AMBER users:
I have used SANDER (amber 8) and NMODE (amber 7) to minimize the
energy of poly[C]-poly[G] RNA with 12 base pairs without sodium ions. It
seems to me that the energies after minimization are different.
Therefore, the calcualted normal modes are different for both cases. I
am not sure whether it is because of the version differences, or the
differnt methods used to minimize the energy in SANDER and NMODE, or
because I have made mistakes to set the control flags. Thank you for
your help very much.
Input file for energy minimization using SANDER
&cntrl
imin=1,
maxcyc=10000000,
ncyc=550000,
ntb=0,
igb=0,
cut=99.0,
dielc=1,
ntpr=100,
drms=0.0001,
ntxo=0,
scee=2.0,
&end
&ewald
eedmeth=5
&end
Final Energy after mininization using SANDER
step = 0
F = -0.904190E+03 GRDMAX = 0.677208E-03 GNORM = 0.996493E-04
E-NONB E-ELE E-HBOND E-BOND
-0.39704E+03 -0.73444E+03 0.00000E+00
0.28200E+02
E-ANGLE E-DIHED E-NB14 E-EEL14
0.14261E+03 0.54218E+03 0.25738E+03
-0.74308E+03
E-POL E-3BOD
0.00000E+00 0.00000E+00
The input file for energy minimization using NMODE
&data
ntrun=4,
nsave=1,
ndiag=2,
cut=99.0,
nprint=10,
drms=0.0001,
maxcyc=80000,
scnb=2.0,
scee=2.0,
ntxo=0,
&end
The energy after minimization using NMODE
step = 0
F = -0.890503E+03 GRDMAX = 0.690726E-03 GNORM = 0.999473E-04
E-NONB E-ELE E-HBOND E-BOND
-0.36385E+03 -0.69668E+03 0.00000E+00
0.27845E+02
E-ANGLE E-DIHED E-NB14 E-EEL14
0.11832E+03 0.55368E+03 0.23530E+03
-0.76512E+03
E-POL E-3BOD
0.00000E+00 0.00000E+00
--
David (Xiaowei) Li
Charles L. Brown Electrical and Computer Engineering
University of Virginia
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Received on Fri Nov 12 2004 - 22:53:00 PST
