Constraint

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constraint is a top level plop command used to specify energetic constraints such as bonds, angles or dihedrals. Note that these constraints can make use of points in space in addition to atoms.

Contents

[edit] Specifying atoms and atom groups

Formats for <atom group 1>

atom <atom_name>                  : Select one atom - atom A:1:_CA_
file <filename>                   : Read in from an external list formated one atom per line in standard Chain:Res:Atom format: "A:1:_CA_"
<type_of_atom> <reslist(2 words)> : Select a set of atoms using plops get_atom_list subroutine: "side A:1 A:1"

Formats for <atom group 2 or xyz Pos> (in addition to those for <atom group 1>)

current                     : Set constraint point to current pos of <atom group 1> 
xyz <x pos> <y pos> <z pos> : Set contraint to constant xyz position: "xyz 1.2 2.3 3.4"

[edit] Distance/Bond Constraints

Creates a spring between COM (center of mass) of atom group 1 and COM of atom group 2

constraints <atom group 1> <atom group 2 or xyz pos> <strength of force in kcals/mol/A> <equilibrium distance (A)>

[edit] Specifying distances

Formats for <equilibrium distance> (No spaces within this format)

<value>           : Equilibrium distance as a single value
<value>+-<slack>  : Equilibrium distance is from <value> + <slack> to <value> - <slack>
<value>+          : Equilbrium distance is any value greater than <value>
<value>-          : Equilbrium distance is any value less than <value>
<value>+<v1>-<v2> : Equilbrium distance is from <value> + <v1> to <value> - <v2>

Examples:

 #constraint from atom _CA_ in residue 1 of chain A to atom _FE_ in residue 3 of chain ' ', equilibrium distance of 2.4 angstroms, force constant of 300 kcal/mol/angstrom
 constraints atom A:1:_CA_ atom _:3:_FE_ 300 2.4

 #constraint from atom _CA_ in residue 1 of chain A, to the point (1.0,2.0,3.0), equilibrium distance of 2.4 plus or minus 0.5 angstroms, force constant of 300 kcal/mol/angstrom
 constraints atom A:1:_CA_ xyz 1.0 2.0 3.0 300 2.4+-0.5

 #?, equilibrium distance is any value greater than 2.4 angstroms, force constant of 300 kcal/mol/angstrom
 constraints side A:1 A:1 xyz 1.0 2.0 3.0 300 2.4+

 #constraint from atom _CA_ in residue 1 of chain A, to its current location, equilibrium distance of (2.4-0.1,2.4+0.2) angstroms, force constant of 300 kcal/mol/angstrom
 constraints atom A:1:_CA_ current 300 2.4+0.2-0.1

Specialized Syntax: This syntax can also be used for constraints involving one atom constrained to its current position (if it is given multiple atoms it will use multiple constraints)

constraints to_current <atom group1> <force kcal/mol/A> ex "constraints to_current calpha all res 10"

For the specific case of expanding binding sites:

constraints binding_site <type_of_atom on ligand> <reslist of ligand (2words)> <radius> <type of atom on receptor> <max displacement> <force kcalc/mol/A>
constraints binding_site heavy Z:999 Z:999 5.0 calpha -10.0

[edit] Angle Constraints

Note: numbers preceded by a D are interpreted as degrees

constraints angle <atom1> <atom2> <atom3> <force kcals/mol/rad> <equilibrium angle>
constraints angle A:1:_CA_ A:1:_CB_ C:1:_H1_ 10.0 1.5708 
constraints angle A:1:_CA_ A:1:_CB_ C:1:_H1_ 10.0 D60.0 
constraints angle A:1:_CA_ A:1:_CB_ C:1:_H1_ 10.0 D60.0+-5.0

[edit] Torsional Constraints

constraints torsion <atom1> <atom2> <atom3> <atom4> <force kcals/mol/rad> <equilibrium rad>
constraints torsion A:1:_CA_ A:1:_CB_ A:1:_CG_ A:1:_CD_ 10.0 0

[edit] Torsion Constraints

Angle between two planes (3 and only three atoms should be in each plane) constraints plane_angle <atoms in plane 1> <atoms in plane 2> <force kcals/mol/rad> <equilibrium rad> Note: numbers preceded by a D are interpreted as degrees

constraints plane_angle A:1:_C1_ A:1:_C3_ C:1:_C5_ B:1:_C1_ B:1:_C3_ B:1:_C5_ 1.0 0.0

[edit] Torsion and Distance Between Planes

Angle and Distance between two planes (3 and only three atoms should be in each plane)

constraints planes <atoms in plane 1> <center/atom> <atoms in plane 2> <center/atom> &
Gaussian <well depth> <full width at half height for angle (rad)> <equil for angle (rad)> &
<full width at half height for dist perpendicular to plane 1 (A)> <equil for dist (rad)> &
<full width at half height for dist parallel to plane 1 (A)> <equil for dist (rad)> 

Same as previous except either the geometric center ('center) or the first atom ('atom') defining the plane is also used for a distance constraint. Designed to be used with gaussian constraints (see below)

constraints planes A:1:_C1_ A:1:_C3_ C:1:_C5_ center B:1:_C1_ B:1:_C3_ B:1:_C atom Gaussian 4.0 D20.0 0.3 4.0 0.3 0.0

[edit] Point to Plane Constraint

Angle between a plane and a point (3 and only three atoms should be in each plane)

constraints pt_plane <atoms in plane 1> <center/atom> <atoms for points use syntax above for atom constraints> &
Gaussian &
 <full width at half height for dist perpendicular to plane 1 (A)> <equil for dist (rad)> &
 <full width at half height for dist parallel to plane 1 (A)> <equil for dist (rad)>

Same as previous except either the geometric center ('center) or the first atom ('atom') defining the plane is also used for a distance constraint. Designed to be used with gaussian constraints (see below)

constraints pt_plane A:1:_C1_ A:1:_C3_ C:1:_C5_ center atom A:1:_C5_ Gaussian 4.0 0.3 4.0 0.3 0.0

Note: numbers preceded by a D are interpreted as degrees

constraints torsion A:1:_CA_ A:1:_CB_ A:1:_CG_ A:1:_CD_ D1.0 D180
constraints torsion A:1:_CA_ A:1:_CB_ A:1:_CG_ A:1:_CD_ D1.0 D180+-10
constraints torsion A:1:_CA_ A:1:_CB_ A:1:_CG_ A:1:_CD_ D1.0 current

Gausian Constraints For some of the above constraints gaussian constraints can be used as well. Replace

<force kcas/mol/(rad or A)>

with

gaussian <well depth (kcal/mol> <full width at half height (rad or A)>

The <equilibrium (rad or A)> term stays the same.

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