modified on 11 September 2014 at 15:03 ••• 1,504 views

Release66:QMMM Appendix

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Format of NWChem parameter file

The format of NWChem parameter is illustrated on the figure below and also available as pdf file.

Format of NWChem parameter file


Conversion of standard AMBER program parameter files

Fortran code that performs conversion from AMBER program parameter file format to NWChem can be found here. It works by parsing out free format AMBER style parameter file contained in amber.in

MASS
C  12.01
CA    12.01
BOND
#this is a comment
C -CA  469.0    1.409           this is also a comment
C  -   CB     447.0      1.419  
ANGLE
C -CA-CA    63.0      120.00 another comment
C -CB-NB    70.0      130.00
DIHEDRAL
X -C -CA-X    4   14.50        180.0             2.         intrpol.bsd.on C6H6
 X - C -  CB -X    4   12.00        180.0             2.         intrpol.bsd.on C6H6
IMPROPER
X -CT-N -CT         1.0          180.          2.           JCC,7,(1986),230
CT -O  - C -OH         10.5         180.           2.
NONBOND
 CA 1.9080  0.0860
C 1.9080  0.0860

to fixed format NWChem style amber.par file

#Generated amber.par file
Electrostatic 1-4 scaling factor     0.833333
Relative dielectric constant     1.000000
Parameters epsilon R*
#
Atoms
CA     12.01000 3.59824E-01 1.90800E-01                            1 1111111111
              6 1.79912E-01 1.90800E-01
C      12.01000 3.59824E-01 1.90800E-01                            1 1111111111
              6 1.79912E-01 1.90800E-01
Bonds
C    -CA      0.14090 3.92459E+05
C    -CB      0.14190 3.74050E+05
Angles
C    -CA   -CA      2.09440 5.27184E+02
C    -CB   -NB      2.26893 5.85760E+02
Proper dihedrals
     -C    -CA   -        3.14159 1.51670E+01    2
     -C    -CB   -        3.14159 1.25520E+01    2
Improper dihedrals
     -CT   -N    -CT      3.14159 4.18400E+00    2
CT   -O    -C    -OH      3.14159 4.39320E+01    2
End