Example: Topology of a Leucine Amino Acid

The following example shows how to set up a Leu amino acid:

     
TOPOlogy
   MASS   H      1.008 
   MASS   C     12.011 
   MASS   CH1E  13.019 
   MASS   CH2E  14.027 
   MASS   CH3E  15.035 
   MASS   N     14.0067 
   MASS   O     15.9994 

   AUTOgenerate ANGLes=TRUE END

   RESIdue LEU
     GROUp
     ATOM N    TYPE=NH1   CHARge=-0.35   END
     ATOM H    TYPE=H     CHARge= 0.25   END
     ATOM CA   TYPE=CH1E  CHARge= 0.10   END
     ATOM CB   TYPE=CH2E  CHARge= 0.00   END
     ATOM CG   TYPE=CH1E  CHARge= 0.00   END
     ATOM CD1  TYPE=CH3E  CHARge= 0.00   END
     ATOM CD2  TYPE=CH3E  CHARge= 0.00   END
     ATOM C    TYPE=C     CHARge= 0.55   END  
     ATOM O    TYPE=O     CHARge=-0.55   END  

     BOND N    CA
     BOND CA   C
     BOND C    O
     BOND N    H
     BOND CA   CB
     BOND CB   CG
     BOND CG   CD1
     BOND CG   CD2

     DIHEdral N    CA   CB   CG
     DIHEdral CA   CB   CG   CD2  

     IMPRoper CA   N    C    CB  
     IMPRoper CG   CD2  CD1  CB  

     DONOr H    N
     ACCEptor O C
   END 
END