# Constraint

### From Jacobson Lab Wiki

**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.