Dear amber users:
I am trying to perform normal mode analysis after energy
minimization using SANDER. But I met following problem:
***************** ***************** *****************
step = 0
F = -0.285807E+03 GRDMAX = 0.192852E+01 GNORM = 0.431100E+00
E-NONB E-ELE E-HBOND E-BOND
-0.37231E+03 -0.32143E+03 0.00000E+00
0.10605E+02
E-ANGLE E-DIHED E-NB14 E-EEL14
0.80886E+02 0.37009E+03 0.14107E+03
-0.19473E+03
E-POL E-3BOD
0.00000E+00 0.00000E+00
Root-mean-square gradient of input coords is 0.431099703381535
This is greater than the requested maximum: 1.00000000000000D-004
The input engergy minimization using SANDER
&cntrl
imin=1,
maxcyc=500000,
ncyc=250000,
ntb=0,
igb=0,
cut=999,
dielc=4,
ntpr=50,
ntr=0,
drms=0.00001,
ntxo=0,
&end
&ewald
eedmeth=5
&end
The output from sander after energy minimization
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
342250 -4.1562E+02 8.9638E-06 6.1266E-05 C3' 209
BOND = 10.6048 ANGLE = 80.8864 DIHED =
370.0898
VDWAALS = -372.3060 EEL = -321.4318 HBOND =
0.0000
1-4 VDW = 141.0750 1-4 EEL = -324.5417 RESTRAINT =
0.0000
The input for normal mode analysis using NMODE
&data
ntrun=1,
cut=999,
drms=0.0001,
dielc=4,
idiel=0,
ntx=0,
&end
Thanks for your help.
Best,
--
Xiaowei Li
Department of Electrical and Computer Engineering
University of Virginia
924-3446(O)
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Received on Thu Oct 14 2004 - 23:53:00 PDT
