Modar internal command:

 restrain

To add restraint terms to MD system, the energy function is in quadratic form as shown bellow for most of restraint type in Modar, except the “wall” case.

 

  • Syntax
     
    restrain <restraint type> <argument>  ...

  • General arguments

    Kforce=<real>

    The force constant k

    initnow=<bool>

    Whether to assign reference value from current structure or not if the reference value is not specified. Default value is true.


  • Restraint type and examples
    • position

      Position restraint, can be applied to atoms or residues individually, or whole group selected.

      #apply a weak restrain to backbone atoms

      restrain postion  Kforce=0.5 applyto=atom \

                  select=”segn PROA && name C CA N O”

       

      #keep protein around its initial position

      restrain postion Kforce=5 select=”segn PROA”


    • dist/distance

      Restrain displacement between two groups. The reference value will be the value from the initial structure if no reference value specified.

      #restrain displacement between two groups

      restrain dist  Kforce=10 select=”segn PROA 11” \                                           select=”segn PROA 31” initnow=false

      • Arguments

        selection=<select expr>

        Target atoms

        kforce=<real>

        Force const of restraint

        Refvalue=<real>

        Reference value, the default value will be retrieved from starting structure if not told.


    • dist2line

      Restrain displacement to a line for groups. The reference value will be the value from the initial structure if no reference value specified for one group restraint case, otherwise the reference value must be told initialy.

      #restrain distance to Z axis

      restrain dist2line lineorg=”0,0,0” linevec=”0,0,1” \

                       Applyto=”residue” \

       Kforce=10 select=”segn ILS”

      • Arguments

        lineorg=<position>

        Tell the point of line resident

        linevec=<vector>

        Tell the direction of line

        applyto=<type>

        Current only “residue” or empty available

        “residue” means applying the restraint to all residues individually for the selections.

        empty means applying the restraint to whole selections

        selection=<select expr>

        Target atoms

        kforce=<real>

        Force const of restraint

        Refvalue=<real>

        Reference value, the default value will be retrieved from starting structure if not told.


    • dist2plane

      Restrain displacement to a plane for groups. The reference value will be the value from the initial structure if no reference value specified for one group restraint case, otherwise the reference value must be told initialy.

      #restrain distance to XY plane

      restrain dist2plane point=”0,0,0” vec=”0,0,1” \

                       Applyto=”residue” \

       Kforce=10 select=”segn ILS”

      • Arguments

        point=<position>

        Tell the point of plane resident

        linevec=<vector>

        Tell the normal vection of line

        applyto=<type>

        Current only “residue” or empty available

        “residue” means applying the restraint to all residues individually for the selections.

        empty means applying the restraint to whole selections

        selection=<select expr>

        Target atoms

        kforce=<real>

        Force const of restraint

        Refvalue=<real>

        Reference value, the default value will be retrieved from starting structure if not told.


    • Zcom

      Z component restraint between two groups. The reference value will be the value from the initial structure if no reference value specified.

      #restrain displacement between two groups in Z direction

      restrain zcom  Kforce=10 select=”segn lip” \                                            select=”segn ben 1”

      • Arguments

        selection=<select expr>

        Target atoms

        kforce=<real>

        Force const of restraint

        Refvalue=<real>

        Reference value, the default value will be retrieved from starting structure if not told.

    • Ycom

      Y component restraint between two groups. The reference value will be the value from the initial structure if no reference value specified.

      #restrain displacement between two groups in Z direction

      restrain ycom  Kforce=10 select=”segn lip” \                                            select=”segn ben 1”

      • Arguments

        selection=<select expr>

        Target atoms

        kforce=<real>

        Force const of restraint

        Refvalue=<real>

        Reference value, the default value will be retrieved from starting structure if not told.

    • Xcom

      X component restraint between two groups. The reference value will be the value from the initial structure if no reference value specified.

      #restrain displacement between two groups in Z direction

      restrain xcom  Kforce=10 select=”segn lip” \                                            select=”segn ben 1”

      • Arguments

        selection=<select expr>

        Target atoms

        kforce=<real>

        Force const of restraint

        Refvalue=<real>

        Reference value, the default value will be retrieved from starting structure if not told.

    • angle

      Angle restraint among three groups. The reference value will be the value from the initial structure if no reference value specified.

      #restrain displacement between two groups

      restrain angle  Kforce=10 select=”segn PROA 11” \

                                select=”segn PROA 31” \

          select=”segn PROA 41” \

      • Arguments

        selection=<select expr>

        Target atoms

        kforce=<real>

        Force const of restraint

        Refvalue=<real>

        Reference value in degree, the default value will be retrieved from starting structure if not told.

    • dihe/dihedral
      Dihedral ngle restraint defined by four groups. The reference value will be the value from the initial structure if no reference value specified.

      #restrain displacement between two groups

      restrain dihe  Kforce=10 select=”segn PROA 11” \

                               select=”segn PROA 31” \

                               select=”segn PROA 41” \                          select=”segn PROA 51”

      • Arguments

        selection=<select expr>

        Target atoms

        kforce=<real>

        Force const of restraint

        Refvalue=<real>

        Reference value in degree, the default value will be retrieved from starting structure if not told.


    • RMSD

      Restrain target RMSD at a certain value reference to ref1; It needs two selection expression, one for superimpose and the other one for RMSD calculation if the part for calculation is not same as the part for superimposing. The reference value must be specified.

      #restrain RMSD reference ref1 

      restrain RMSD  Kforce=10 select=”segn PROA && not hydrogen”
      • Arguments

        selection=<select expr>

        Target atoms

        kforce=<real>

        Force const of restraint

        Refvalue=<real>

        Reference value in degree, the default value will be computed according to starting structure if not told.


    • dRMSD

      Restrain the difference between RMSD to ref1 and RMSD to ref2. Sharing the same syntax form with RMSD, but needs both reference coordinates buffers REF1 and REF2 to be initiated.

      #restrain RMSD reference ref1

      restrain dRMSD  Kforce=10 select=”segn PROA && not hydrogen”

      • Arguments

        selection=<select expr>

        Target atoms

        kforce=<real>

        Force const of restraint

        Refvalue=<real>

        Reference value in degree, the default value will be computed according to starting structure if not told.


    • zRange

      Restrain targets in Z range, it can be applied to residues individually, or whole group selected. Only needs one selection expression. The start and end position must be specified.

      #restrain ILC in Z range

      restrain zRange  applyto=residue Kforce=10 startpos=-20 endpos=20 \                 select=”segn ILC”

      • Arguments

        selection=<select expr>

        Target residues or group

        kforce=<real>

        Force const of restraint

        startpos=<real>

        endpos=<real>

        Range

    • zBlock

      Restrain target outside of a Zrange, i.e. to block target moving to the range specified. Sharing the command form with Zrange.

      #block water outside of a Z range

      restrain zBlock  applyto=residue Kforce=10 startpos=-20 endpos=20 \                       select=”segn WAT”

      • Arguments

        selection=<select expr>

        Target residues or group

        kforce=<real>

        Force const of restraint

        startpos=<real>

        endpos=<real>

        Range


    • zWall

      A Lennard-Jones Potential mimicking wall for separating two gradients. Only needs one selection expression. The wall position and repulsion cutoff, switch cutoff must be specified.

      #separate water and ILC by Waals

      #left wall

      restrain zWall  applyto=residue Kforce=10 pos=-20 \

                      cutoff=10 swcutoff=8 \

                      select=”ALL”

      #right wall

      restrain zWall  applyto=residue Kforce=10 pos=20 \

                      cutoff=10 swcutoff=8 \ 

           select=”ALL”
      • Arguments

        selection=<select expr>

        Target residues or group

        kforce=<real>

        Force const of restraint

        pos=<real>

        Wall position

        Cutoff=<real>

        Swcutoff=<real>

        Lenar-Jones repulsion cutoff and switching point


    • sRange

      Restrain target in a cutoff radiation range from a center point, which can be a sphere shell or a sphere. The start and end position must be specified, the default center is at origin.

      #restrain water inside a sphere

      restrain sRange  applyto=residue Kforce=10 startpos=0 endpos=20 \

                       center=(0,0,0) \ 

                       select=”segn WAT”
      • Arguments

        selection=<select expr>

        Target residues or group

        kforce=<real>

        Force const of restraint

        startpos=<real>

        endpos=<real>

        Range

        Center=<position>

        The center position


    • sBlock

      Restrain target outside of a cutoff sphere, i.e. to block target moving to the sphere or the sphere shell specified.

      #restrain water outside a sphere

      restrain sBlock  applyto=residue Kforce=10 startpos=0 endpos=20 \

                       center=(0,0,0) \ 

            select=”segn WAT”
      • Arguments

        selection=<select expr>

        Target residues or group

        kforce=<real>

        Force const of restraint

        startpos=<real>

        endpos=<real>

        Range

        Center=<position>

        The center position


    • sWall

      A Lennard-Jones Potential mimicking wall for separating two gradients. Only needs one selection expression. The wall position and repulsion cutoff, switch cutoff must be specified and the default center is at origin.

      #separate water and a bubble by sphere wall

      restrain rWall  applyto=residue Kforce=10 pos=40 \

                      cutoff=10 swcutoff=8 center=(0,0,0) \ 

                      select=”ALL”
      • Arguments

        selection=<select expr>

        Target residues or group

        kforce=<real>

        Force const of restraint

        pos=<real>

        Wall position

        Cutoff=<real>

        Swcutoff=<real>

        Lenar-Jones repulsion cutoff and switching point

        Center=<position>

        The center position



  • Variables exported
    none




 

 

 

 

 

 

 

 

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