Example: A Polypeptide Chain

The following example file shows how to set up a polypeptide segment (Tyr, Ala, Glu, Lys, Ile, Ala), assuming that the topology and parameters have been previously read. For completeness, the definitions of the patch residues PEPT, PROP, NTER, and CTER have been included. Normally, these patch residues are already defined in the topology files.

 
topology
   PRESidue PEPT 
     ADD BOND -C +N 
     ADD ANGLE -CA -C +N
     ADD ANGLE -O  -C +N
     ADD ANGLE -C  +N +CA
     ADD ANGLE -C  +N +H
     ADD DIHEdral  -C +N +CA +C
     ADD DIHEdral  -N -CA -C +N
     ADD DIHEdral  -CA -C +N +CA
     ADD IMPRoper  -C -CA +N -O  {planar -C}
     ADD IMPRoper  +N -C +CA +H  {planar +N}
   END

   PRESidue PEPP 
     ADD BOND -C +N 
     ADD ANGLE -CA -C +N
     ADD ANGLE -O  -C +N
     ADD ANGLE -C  +N +CA
     ADD ANGLE -C  +N +CD
     ADD DIHEdral  -C +N +CA +C
     ADD DIHEdral  -N -CA -C +N
     ADD DIHEdral  -CA -C +N +CA
     ADD IMPRoper  -C -CA +N -O  {planar -C}
     ADD IMPRoper  +N +CA +CD -C  {planar +N}
  END

  PRESidue NTER  
    GROUp
    ADD    ATOM +HT1  TYPE=HC   CHARge=0.35  END
    ADD    ATOM +HT2  TYPE=HC   CHARge=0.35  END
    MODIfy ATOM +N    TYPE=NH3  CHARge=-0.30 END
    ADD    ATOM +HT3  TYPE=HC   CHARge=0.35  END
    DELETE ATOM +H                           END
    MODIfy ATOM +CA             CHARge=0.25  END
    ADD BOND +HT1 +N
    ADD BOND +HT2 +N
    ADD BOND +HT3 +N
    ADD ANGLe +HT1  +N    +HT2
    ADD ANGLe +HT2  +N    +HT3
    ADD ANGLe +HT2  +N    +CA
    ADD ANGLe +HT1  +N    +HT3
    ADD ANGLe +HT1  +N    +CA
    ADD ANGLe +HT3  +N    +CA
    ADD DIHEdral +HT2  +N    +CA   +C
    ADD DIHEdral +HT1  +N    +CA   +C
    ADD DIHEdral +HT3  +N    +CA   +C
    ADD DONOr +HT1  +N
    ADD DONOr +HT2  +N
    ADD DONOr +HT3  +N
  END

  PRESidue PROP     
    GROUp
    ADD    ATOM +HT1  TYPE=HC   CHARge= 0.35   END
    ADD    ATOM +HT2  TYPE=HC   CHARge= 0.35   END
    MODIfy ATOM +N    TYPE=NH3  CHARge=-0.20   END
    MODIfy ATOM +CD             CHARge= 0.25   END
    MODIfy ATOM +CA             CHARge= 0.25   END
    ADD BOND +HT1  +N
    ADD BOND +HT2  +N
    ADD ANGLe +HT1  +N    +HT2
    ADD ANGLe +HT2  +N    +CA
    ADD ANGLe +HT1  +N    +CD
    ADD ANGLe +HT1  +N    +CA
    ADD ANGLe +CD   +N    +HT2
    ADD DIHEdral +HT2  +N    +CA   +C
    ADD DIHEdral +HT1  +N    +CA   +C
    ADD DONOr +HT1  +N
    ADD DONOr +HT2  +N
  END

  PRESidue CTER     
    GROUp
    MODIfy ATOM -C             CHARge= 0.14  END
    ADD    ATOM -OT1  TYPE=OC  CHARge=-0.57  END
    ADD    ATOM -OT2  TYPE=OC  CHARge=-0.57  END
    DELETE ATOM -O                           END
    ADD BOND -C    -OT1
    ADD BOND -C    -OT2
    ADD ANGLe -CA   -C   -OT1
    ADD ANGLe -CA   -C   -OT2
    ADD ANGLe -OT1  -C   -OT2
    ADD DIHEdral -N    -CA    -C   -OT2
    ADD IMPRoper -C    -CA    -OT2 -OT1
    ADD ACCEptor -OT1 -C
    ADD ACCEptor -OT2 -C
  END
end

segment 
   name="PROT" 
   chain
      link pept head - * tail + * end             
      first prop tail + pro end     ! special n-ter for PRO 
      first nter tail + *   end 
      last cter head - * end
      sequence TYR ALA GLU LYS ILE ALA end
   end
 end

The information about the patch residues is normally included in the topology file. The information about the peptide linkages is also included in the “toph19.pep" file in the “toppar" directory. Wildcards allow one to use the same patch residues (“PEPT") for all combinations of amino acids. The only exception is Pro, which needs a special N-terminal patch. The residues are numbered consecutively, starting with 1. To use a particular numbering for residues, one should use the COOR option to read the sequence from the coordinate file.