[gmx-users] oplsaa galactose

[nishap.patel at utoronto.ca]

Hello,

     I am trying to simulate hexopyronase using OPLS-AA forcefield  
using parameters from the paper:

An improved OPLS?AA force field for carbohydrates, 2002 by Gunsteren.

I was looking through the ffoplsaabon.itp file and there are some  
dihedral parameters for hexopyronase. I am not sure what the comment  
below means.

   Below are extra dihedrals for some special organic molecules.
; Since the atom types are identical to other dihedrals you have to specify
; them explicitly with a define if you happen to simulate this type of  
molecule.

How would I mention it in my rtp file? I don't understand ' specify
them explicitly with a define'  This is my .rtp for Galactose

[ GLA ]
  [ atoms ]
      O    opls_180   -0.400     1
     C1 	  opls_195    0.365     2
     H1    opls_196    0.100     2
     O1    opls_154   -0.683     2
     HO1   opls_155    0.418     2
     C2 	  opls_158    0.205     3
     H2    opls_176    0.060     3
     O2    opls_154   -0.683     3
     HO2   opls_155    0.418     3
     C3 	  opls_158    0.205     4
     H3    opls_176    0.060     4
     O3    opls_154   -0.683     4
     HO3   opls_155    0.418     4
     C4 	  opls_158    0.205     5
     H4    opls_176    0.060     5
     O4    opls_154   -0.683     5
     HO4   opls_155    0.418     5
     C5 	  opls_183    0.170     6
     H5    opls_185    0.030     6
     C6    opls_157    0.145     7
     H61   opls_176    0.060     7
     H62   opls_176    0.060     7
     O6    opls_154   -0.683     7
     HO6   opls_155    0.418     7
  [ bonds ]
      O    C1
      C1   H1
      C1   O1
      O1   HO1
      C1   C2
      C2   H2
      C2   O2
      O2   HO2
      C2   C3
      C3   H3
      C3   O3
      O3   HO3
      C3   C4
      C4   H4
      C4   O4
      O4   HO4
      C4   C5
      C5   C6
      C5   O
      C6   H61
      C6   H62
      C6   O6
      O6   HO6