AMBER Archive (2004)

Subject: AMBER: normal mode analysis after energy minimizaiton using sander

From: xiaowei li (xl3a_at_virginia.edu)
Date: Thu Oct 14 2004 - 16:57:30 CDT

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)

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu