AMBER Archive (2005)

Subject: AMBER: Problem finding transition state using NMODE

From: Peter Anderson (toutvabien78_at_yahoo.com)
Date: Thu Sep 22 2005 - 07:36:00 CDT

Dear Amber Users,

I am trying to use the nmode program of AMBER 8 in
order to find the energy and transition state
separating two minimum-energy structures of a
four-residue peptide in vacuum. In order to test how
it's done, I simply used an input file with contents:

transition-state search
 &data
     ntrun=2,
     cut = 20.,
     ntx = 1,
 &end

using default values for everything else.

I entered the following command:

nmode -O -i nmode.in -o nmode.out -c min1.restrt -p
vac.top -r nmode.restrt

where "min1.restrt" contains the coordinates of one of
the minima.

Some of my output file contains the following:

Getting coordinates from file with title:
     ACE

    Number of non-bonded pairs = 145
    Number of H-bonded pairs = 0

 ***************** *****************
*****************
   step = 0
     F = -0.721358E+01 GRDMAX = 0.120958E+02
GNORM = 0.267754E+01
       E-NONB E-ELE E-HBOND
            E-BOND
    -0.14964E+01 -0.22256E+02
0.00000E+00 0.10024E+01
       E-ANGLE E-DIHED E-NB14
            E-EEL14
     0.27117E+01 0.11183E+02
0.32273E+01 -0.15853E+01
       E-POL E-3BOD
     0.00000E+00 0.00000E+00
     Coordinate origin is now the molecular center of
mass

 ***************** *****************
*****************
   step = 1
     F = -0.721358E+01 GRDMAX = 0.120958E+02
GNORM = 0.267754E+01
       E-NONB E-ELE E-HBOND
            E-BOND
    -0.14964E+01 -0.22256E+02
0.00000E+00 0.10024E+01
       E-ANGLE E-DIHED E-NB14
            E-EEL14
     0.27117E+01 0.11183E+02
0.32273E+01 -0.15853E+01
       E-POL E-3BOD
     0.00000E+00 0.00000E+00
          rms of step length = 0.0971543441
Bad nonbon: 2 8 0.83866E-02 0.13419E+18
Bad nonbon: 2 9 0.83866E-02 0.22748E+19
Bad nonbon: 2 10 0.83866E-02 0.19622E+18
Bad nonbon: 2 11 0.83866E-02 0.22748E+19
Bad nonbon: 2 12 0.83866E-02 0.19622E+18
Bad nonbon: 2 13 0.83866E-02 0.19622E+18
Bad nonbon: 2 14 0.83866E-02 0.19622E+18
Bad nonbon: 2 15 0.83866E-02 0.22748E+19
Bad nonbon: 2 16 0.83866E-02 0.19622E+18
Bad nonbon: 2 17 0.83866E-02 0.19622E+18
Bad nonbon: 2 18 0.83866E-02 0.19622E+18
Bad nonbon: 2 19 0.83866E-02 0.20169E+19
Bad nonbon: 2 20 0.83866E-02 0.13536E+19
Bad nonbon: 2 21 0.10094E+01 0.70423E+06
Bad nonbon: 2 22 0.83866E-02 0.40369E+16
Bad nonbon: 2 23 0.10719E-01 0.92600E+15
Bad nonbon: 3 10 0.00000E+00 INF
Bad nonbon: 3 11 0.00000E+00 INF
Bad nonbon: 3 12 0.00000E+00 INF
[... etc. ...]
          ene @step k-1 = -16.594823 ene @k =
         nan
          ... scaling was unsuccessful ... stop

Can someone please tell me what this "Bad nonbon ....
INF" error means? Also, is there a flag in the
command line which should designate the coordinates of
the second minimum to which my starting structure is
connected?

Thanks for any help you can give.

Peter Anderson

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