AMBER Archive (2004)

Subject: Re: AMBER: Amber Transition State Output

From: Johnson Agbo (agboj_at_chem.unr.edu)
Date: Wed Jun 09 2004 - 19:33:58 CDT

I am using nmode to find a transition state structure(coordinates) and the
energy barrier between my input structure or mininum structure and that of
the transition state. My input structure has 24.0 kcal/mol of energy. The
output file I am looking at has as its last part for the transition state
search as :
   step = 56
      F = -0.488232E+01 GRDMAX = 0.662498E-03 GNORM = 0.132406E-03
        E-NONB E-ELE E-HBOND E-BOND
     -0.20634E+01 -0.28338E+02 0.00000E+00
0.57860E+00
        E-ANGLE E-DIHED E-NB14 E-EEL14
      0.27568E+01 0.45998E+01 0.57571E+01
0.11826E+02
        E-POL E-3BOD
      0.00000E+00 0.00000E+00

Found transition state:

  ***************** ***************** *****************
    step = 56
      F = -0.488232E+01 GRDMAX = 0.662498E-03 GNORM = 0.132406E-03
        E-NONB E-ELE E-HBOND E-BOND
     -0.20634E+01 -0.28338E+02 0.00000E+00
0.57860E+00
        E-ANGLE E-DIHED E-NB14 E-EEL14
      0.27568E+01 0.45998E+01 0.57571E+01
0.11826E+02
        E-POL E-3BOD
      0.00000E+00 0.00000E+00
           b1 = -0.07361 b2 = 0.06656 tlamba = -0.17361
           rms of step length = 0.0577350278
           ene @step k-1 = -4.882317 ene @k = 14.533882
           ene @step k-1 = -4.882317 ene @k = 7.543089
           ene @step k-1 = -4.882317 ene @k = 3.070845
           ene @step k-1 = -4.882317 ene @k = 0.208641
           ene @step k-1 = -4.882317 ene @k = -1.623461
           ene @step k-1 = -4.882317 ene @k = -2.796260
           ene @step k-1 = -4.882317 ene @k = -3.547019
           ene @step k-1 = -4.882317 ene @k = -4.027604
           ene @step k-1 = -4.882317 ene @k = -4.335235
           ene @step k-1 = -4.882317 ene @k = -4.532149
           ene @step k-1 = -4.882317 ene @k = -4.658191
      Coordinate origin is now the molecular center of mass
           b1 = 0.00151 b2 = 0.02023 tlamba = -0.09849
           rms of step length = 0.4152882440
           ene @step k-1 = -4.658191 ene @k = 58.765594
           ene @step k-1 = -4.658191 ene @k = 34.889225
           ene @step k-1 = -4.658191 ene @k = 19.807583
           ene @step k-1 = -4.658191 ene @k = 10.320876
           ene @step k-1 = -4.658191 ene @k = 4.384055
           ene @step k-1 = -4.658191 ene @k = 0.693016
           ene @step k-1 = -4.658191 ene @k = -1.582165
           ene @step k-1 = -4.658191 ene @k = -2.968536
           ene @step k-1 = -4.658191 ene @k = -3.799999
           ene @step k-1 = -4.658191 ene @k = -4.287485
           ene @step k-1 = -4.658191 ene @k = -4.563759

  ***************** ***************** *****************

I hope this helps.
Thanks.

On Wed, 9 Jun 2004, David A. Case wrote:

> On Wed, Jun 09, 2004, Johnson Agbo wrote:
>
>> How is the output file for the transition state interpreted. I cannot
>> locate the barrier height from the results of the output file.
>
> Can you be more specific about what sort of output you are looking at? Is
> this from nmode? Maybe you could post a bit of the output that you find
> hard to interpret, plus a little bit about what you are doing.
>
> ...dac
>
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