Modar internal command:

 segment

To patch or modify a segment.

  • Syntax
     
    segment <subcommand> <argument> ...

  • Examples

    #patching peptide terminals

    segment patch first=NTER last=CTER


  • subcommands:
    Current only “patch” implemented, the patching reside type name need to be told for the terminals.


  • Terminal patching residues
    All available terminus patch for peptide in CHARMM force field

    N terminus

    NTER       

    standard N-terminus

         HT1

    (+)/   

    --N--HT2

         \   

          HT3

    ACE       

    acetylated N-terminus to create dipeptide

       HT1        HY1  

       |             /     

    --N--CY--CAY--HY2

              ||      \     

             O       HY2  

    C Terminus

    CTER       

    acetylated N-terminus for proline dipeptide

            OT2(-)

    /

    ---C

    \\

     OT1

    CT1

    methylated C-terminus from methyl acetate

    OT1             

      //                

    --C          HT1      

        \          /        

        OT2--CT--HT2   

                    \ 

                       HT3

    CT2

    amidated C-terminus                    

         O     HT1

          ||      /  

       --C--NT   

                  \  

                     HT2

    CT3

    N-Methylamide C-terminus                     

       O  HNT      HT1

        ||     |          /

     --C---NT---CAT--HT2

                         \

                          HT3

  • Variables exported
    none



 

 

 

 

 

 

 

 

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