Modar internal command:

 calc

To calculate disance, angle, dihedral ...

  • Syntax
    calc <subcommand>  [arguments] ... [select expr] ...

  • Subcommands and examples:
    • center

      #to compute center of mass of atoms selected

      calc center  select="segn PROA"

      • Variables exported:

        Xce, Yce, Zce

        Center of mass


    • dist/distance

      #to compute distance between two groups

      calc dist  select="reside PROA 1" select=”reside PROA 100”
      • Variables exported:

        Value

        The distance between two groups

    • dist2line

      #to compute distance to Z axis

      calc dist2line  lineOrg=”0,0,0” lineVec=”0,0,1” select="reside PROA 1"

      • Variables exported:

        Value

        The distance to the line specified

    • dist2plane

      #to compute distance to XY plane

      calc dist2plane  point=”0,0,0” vec=”0,0,1” select="reside PROA 1"

      • Variables exported:

        Value

        The distance to the plane specified

    • Zcom

      #to compute z distance between two groups

      calc zcom  select="reside PROA 1" select=”reside PROA 100”
      • Variables exported:

        Value

        The z distance between two groups

    • Ycom

      #to compute y distance between two groups

      calc ycom  select="reside PROA 1" select=”reside PROA 100”
      • Variables exported:

        Value

        The Y distance between two groups

    • Xcom

      #to compute X distance between two groups

      calc xcom  select="reside PROA 1" select=”reside PROA 100”
      • Variables exported:

        Value

        The Z distance between two groups

    • angle

      #to compute angle

      calc dist  select="reside PROA 1" \

                 select=”reside PROA 10” \

                 select=”residue PROA 20”

      • Variables exported:

        Value

        The angle value in degree


    • dihe/dihedral

      #to compute dihedral

      calc dihe group1="atom PROA 49 C" \

      group2="atom PROA 50 N" \

      group3="atom PROA 50 CA" \

      group4="atom PROA 50 C"

      • Variables exported

        Value

        The dihedral value in degree


    • rgy

      #to compute radius of gyration for atoms selected

      calc rgy  select="segn PROA"

      • Variables exported:

        Value

        Radius of gyration



    • zrgy

      #to compute radius of gyration, Z component only

      calc zrgy select="segn ILC"

      • Variables exported:

        Value

        Radius of gyration



    • orient

      #to compute primary axis of atoms selected

      calc orient  select="segn PROA"

      • Variables exported:

        Xax, Yax, Zax

        Primary axis of rigid body



    • rmsd

      #to compute RMSD

      calc rmsd fitgroup="segn PROA && name C CA N O" \

      calcgroup=”segn PROA”

      note: the reference need to be loaded first, please see command "loadcrd" for more detail.
      • Variables exported:

        Value

        The RMSD computed


    • voltage

      #to compute voltages for points

      calc voltage start=(0,0,-60) end=(0,0,60) stride=(0,0,0.1) \

           outfile=”volt.txt”

       

      #to compute voltages for points from file

      calc voltage inxyzfile=”grids.txt” outfile=”volt.txt”

      • Variables exported:
        none

 

 

 

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