CONSTRAINTS The following forms of constraints are available in CHARMM: * Menu: command * Harmonic Atom:: "CONS HARM" Hold atoms in place * Dihedral:: "CONS DIHE" Hold dihedrals near selected values * Internal Coord:: "CONS IC" Holds bonds, angles and dihedrals near table values * Quartic Droplet:: "CONS DROP" Puts the entire molecule in a cage about the center of mass * RMSD restraints: "RMSD" Holds atoms in place relative to reference structure/structures * Fixed Atom:: "CONS FIX" Fix atoms rigidly (sets the IMOVE array) * Center of Mass:: "CONS HMCM" Constrain center of mass of selected atoms * SHAKE:: "SHAKE" Fix bond lengths during dynamics. * NOE:: "NOE" Impose distance restraints from NOE data * Restrained Distances:: "RESD" Impose general distance restraints * External Forces:: "PULL" Impose externally applied (pulling) force * Rg/RMSD restraint:: "RGYR" Impose radius of gyration or rmsd restraint * Distance Matrix restraint:: "DMCO" Impose a distance matrix restraint * Sbound: (sbound.doc). Solvent boundary potential

Holding atoms in place ------------------------------------------------------------------------------ [SYNTAX CONS HARMonic] Syntax: CONS HARMonic {[ABSOlute] absolute-specs force-const-spec coordinate-spec } { BESTfit bestfit-specs force-const-spec coordinate-spec } { RELAtive bestfit-specs force-const-spec 2nd-atom-selection} { CLEAr } force-const-spec ::= { FORCE real } atom-selection [MASS] { WEIGhting } absolute-specs ::= [EXPOnent int] [XSCAle real] [YSCAle real] [ZSCAle real] bestfit-specs ::= [ NOROtation ] [ NOTRanslation ] coordinate-spec::= { [MAIN] } { COMP } { KEEP } The potential energy has a harmonic restraint term which allows one to prevent large motions of individual atoms. There are three forms for this restraint, ABSOLUTE, BESTFIT, and RELATIVE. It is possible to combine multiple restraints in one energy calculation, but no atom may participate in more than one harmonic restraint set. ------------------------------------------------------------------------------ ABSOLUTE positional restraints. Absolute positional restraints specify a location a cartesian space where an atom must remain proximal. This is the original positional restraint in CHARMM. The form for this potential is as follows for coordinates: EC = sum over selected atoms of k(i)* [mass(i)] * (x(i)-refx(i))**exponent where refx is a reference set of coordinates. If MASS is specified in the command line, then k is multiplied by the mass of the atom resulting in a natural frequency of oscillation for the restraint of sqrt(k) in AKMA units. An atom restrained with MASS FORCE 1.0 will oscillate at 8 cycles/picosecond if free of other interactions. For most operations involving harmonic restraints, mass weighting is recommended. There are three reasons for this. First, the results obtained will be similar regardless of what atom representation is used (extended vs. explicit) for hydrogen atoms. Second, Hydrogen atoms are allowed greater relative freedom if present. And third, The character of the normal modes of a molecule are unperturbed with mass weighting (essential if normal modes or low frequency motions are of interest). Note, there is no longer a prefactor of 0.5 on the force constant specification. This is appropriate in that exponent values other than "2" are allowed. This differs from the earlier versions of CHARMM (up to version 16). The restraint force constant can be set to any positive value (specified by the FORCE keyword followed by the desired value). The force constants may also be obtained from the weight array, in which case the FORCe keyword is not read. When using this option, a negative values may be used for some atoms, however, the total weight must be positive. The reference coordinates can be the current set at the point when restraints are specified (the default) or a set can be the comparison set (COMP keyword). When multiple CONS HARM commands are used, the KEEP option preserves the reference coordinates from the previous restraints. This is useful in cases where the force constant is to be modified, but no other changes are desired. The variables XSCAle, YSCAle, and ZSCAle are global scale factors for ABSOLUTE harmonic restraint terms. The default scale factor is 1.0 for all terms. If multiple harmonic restraint sets are used, they may have different scale factors. The RELATIVE and BESTFIT types do not allow a scale factor at present. Example: CONS HARM FORCE 1.0 MASS SELE atom * * CA END COMP This command harmonically restrains all alpha-carbons to the current positions in the comparison coordinates with a force constant of 24 Kcals/mol/A**2 (assuming a mass of 12). ------------------------------------------------------------------------------ BESTFIT positional restraints This restraint is similar to the absolute restraints except that the reference coordinates are (implicitly) rotated and translated so as to bestfit the selected atoms. This best fit is done in a manner that minimizes the restraint energy. Due to the nature of the best fit, this restraint term does not add any net force or torque to the system. Note 1: An exponent may not be specified (it is set to 2) Note 2: Global scale factors do not apply Note 3: At present, there is no Hessian code for this restrain Note 4: There is no energy partition (ANAL command) for this restraint Example: CONS HARM BESTFIT MASS FORCE 1.0 COMP SELE SEGID A END CONS HARM BESTFIT MASS FORCE 1.0 COMP SELE SEGID B END These commands will restrain segments A and B to the geometries they have in the current comparison coordinates. This restraint will not add a net force or torque to the system (unlike the ABSOLUTE restraint type). Segments A and B can move (rotate/translate) independently with no change in the restraint energy. See also CONS RMSD below. ------------------------------------------------------------------------------ RELATIVE positional restraints. The relative positional restraints are similar to the bestfit restraint except there is no reference coordinates. In this case, one part of the system is restrained to have the same shape as another part of the system. The two restraint sets are implicitly bestfit by an optimal rotation/translation (minimizing the restraint energy). Both sets of atoms Note 1: An exponent may not be specified (it is set to 2) Note 2: Global scale factors do not apply Note 3: At present, there is no Hessian code for this restrain Note 4: There is no energy partition (ANAL command) for this restraint Note 5: The atoms of the two sets are matched on-to-one in sequential order. Note 6: If the two sets do not have the same number of atoms, an error will be issued and the set lists will be truncated. Note 7: Both sets must be specified and must not use set number 1. Example: CONS HARM RELATIVE WEIGHT SELE segid a1 END SELE segid a2 END NOROT NOTRAN This command will force two replicas (A1 and A2) to have the same coordinates based on the values in the weighting array (as best fit weights). Example: CONS HARM RELATIVE MASS FORCE 10.0 SELE SEGID A END SELE SEGID B END This command will force two segments (A and B) to have the same shape, but they may have very different locations and orientations. Atoms are matched one-to-one by selected atom number. ------------------------------------------------------------------------------ GENERAL INFORMATION It is important to understand some aspects of how the restraints are set in order to get the most flexibility out of this command. When CHARMM is loaded, each atom has associated with it a harmonic force constant initially set to zero. Each call to the CONS HARM command changes the value of this constant for only those atoms specified. When this command is invoked with an atom selection (and KEPP is not specified), only the reference coordinates (XREF,YREF,ZREF) for selected atoms are modified. IMPORTANT NOTE: Each atom may participate in AT MOST one harmonic restraint term. This is a coding limitation designed to maximize compatibility with older CHARMM scripts (i.e. doing a series of minimizations with a decreasing series of force constants). This could be easily modified with a bit of work to increase the capability (at the expense of script compatibility). When multiple restraint sets are used, it is important to note that all selections should be exclusive. When they are not exclusive, then atoms will be assigned to the restraint of the most recent CONS HARM command which selected that atom. In other words, the restraint set number is an atomic property. If restraint sets are broken up, then an error message will be issued. If an entire set is replaced, then the new restraint replaces the old one (without a warning message). ------------------------------------------------------------------------------ OTHER COMMANDS: The harmonic restraints may no longer be read and written to files. The PRINT command still functions for harmonic restraints for information. To examine or modify the internal harmonic restrain data, the SCALar command (arrays: CONStraints,XREF,YREF, and ZREF) may be used (see *Note scalar::(chmdoc/scalar) ). In addition, one may look at the contributions to the energy in detail using the ANALysis command, see *note anal:(chmdoc/analys). ------------------------------------------------------------------------------

Holding dihedrals near selected values Using this form of the CONS command, one may put restraints on the dihedral angles formed by sets of any four atoms. The improper torsion potential is used to maintain said angles. The command for setting the dihedral restraints is as follows: Syntax: [SYNTAX CONS DIHEdral] CONS DIHEdral [BYNUM int int int int] [FORCe real] [MIN real] [PERIod int] [ atom-selection ] [ COMP ] [WIDTh real] [ 4X(atom-spec) ] [ MAIN ] CONS CLDH Syntactic ordering: DIHE or CLDH must follow CONS, and FORCE, MIN and PERIod must follow DIHE. where: atom-spec ::= { segid resid iupac } { resnumber iupac } DIHEdral adds a torsion angle to the list of restrained angles using the specified atoms, force constant, minimum and periodicity. If an atom selection is used, then the first 4 selected atoms (in order) will define the dihedral angle. If either MAIN or COMP is specified and [MIN real] is not, then the minimum angle value will be determined by the current dihedral angle value in the corresponding coordinate set. If the PERIodicity is zero (improper type), then the force constant has units of kcal/mol/radian/radian, else it has units of kcal/mol. Ecdih = FORCE * max(0, abs( phi - MIN*pi/180) - WIDTH)**2 [ PERIod = 0 ] Ecdih = FORCE * (1-cos( PERIod* (phi - MIN*pi/180 )) ) [ PERIod > 0 ] CLDH clears the list of restrained dihedrals so that different angles or new restraint parameters can be specified. Other commands: The PRINT CONS command, see *note print:(io.doc)print, will work for restraints.

Holding Internal Coordinates near selected values [SYNTAX CONS IC] Syntax: CONStraint IC [BOND real [EXPOnent integer] [UPPEr]] [ANGLe real] [DIHEdral real] [IMPRoper real] Using this form of the CONS command, one may put restraints on any internal coordinate. For this energy term, the IC table is used. At each energy call, the reference (zero-force) value of each IC is set to the value currently in the IC table. All nonzero bond entries are restrained with the bond constant, using the optional EXPOnent (default 2) in the potential K*(S-S0)**EXPOnent. Second derivatives are currently supported only with EXPOnent=2. The angle, dihedral, and improper terms are only harmonic. The DIHEdral term only applies to IC's of normal type, and the IMPRoper term only applies to the improper IC type (those with a "*") If UPPEr is specified the reference bond length is taken as an upper limit and the restraint potential is applied only if S>S0; this is intended for use with distance restraints from NMR NOE data. All nonzero angle entries are restrained with the angle constant. All dihedrals are restrained with the dihedral constant using the improper dihedral energy potential. If any IC entry contains an undefined atom (zeroes), then the associated bonds,angles, and dihedral will not be restrained. The force constant has units of kcal/mol/radian/radian for both angle and dihedral restraints. The bond force constant has units of kcal/mol/angstrom**EXPOnent. This restraint term is very flexible in that the user may chose which bonds... to restrain by editing an IC table. The major drawback is that all bonds must have the same force constant. The same is true for angles and dihedrals. By listing some IC's several times, the effective force constant is increased. Also, if only angle restraints are desired, then the bond and dihedral constants can be set to zero eliminating their contribution.

The Quartic Droplet Potential [SYNTAX CONS DROPlet] Syntax: CONStraint DROPlet [FORCe real] [EXPOnent integer] [NOMAss] This restraint term is designed to put the entire molecule in a cage. Is is based on the center of mass (or center of geometry if NOMAss is specified) so that no net force or torque is introduced by this restraint term. The potential function is; Edroplet= FORC* sum over atoms (( r-rcm )**EXPO )*mass(i))

How to fix atoms rigidly in place [SYNTAX CONS FIX] Syntax: CONS FIX atom-selection-spec { [PURG] } { [BOND] [THET] [PHI] [IMPH] } This command will fix all selected atoms and unfix all non-selected atoms. For example, the command; CONS FIX SELE NONE END will remove all fixing of atoms (except for lonepairs). This command fixes atoms in place by setting flags in an array (IMOVE) which tells the minimization and dynamics alogrithms which atoms are free to move. If atoms are fixed, it is possible to save computer time by not calculating energy terms which involve only fixed atoms. The nonbond and hydrogen bond algorithms in CHARMM check IMOVE and delete pairs of atoms that are fixed in place from the nbond and hbond lists respectively. In addition the PURG or individual energy term options specified with the CONS FIX command allow all or some of the internal coordinate energies associated with fixed atoms to be deleted. Interactions between fixed and moving atoms are maintained. *** NOTE *** because some energy terms are deleted from fixed systems, the total energy calculated with fixed atoms will be different from the total energy of the same system with all atoms free. The forces on the moveable atoms will however be identical. The purpose of this feature is to remove the computational cost of energy terms that do not change for simulations where a large fraction of the atoms are fixed. It is not recommended for any other purpose. The way CHARMM keeps track of fixed atoms is by the IMOVE array in the PSF. The IMOVE array is 0 if the atom is free to move, and has the value 1 if it is fixed. A value of -1 indicates that this atom is a lonepair. ***** WARNING ***** The purge options modify the PSF. The effects of this command cannot be undone by the subsequent releasing of atoms. ***** WARNING ***** The fixing of atoms does not work for constant pressure simulations.

Constrain centers of mass for selected atoms [SYNTAX CONS HMCM] Syntax: CONS HMCM FORCe real [WEIGhting] reference-spec atom-selection where: reference-spec ::= REFX real REFY real REFZ real This command will harmonically restrain centers of mass from the selected atoms to the absolute reference point specified with REFX, REFY and REFZ. The force constant of the harmonic potential is set with the FORCe keyword. Mass weighting is switched off by default but can be selected by using the WEIG key. The primary use of this command is during the reconstruction of all-atom representations from low resolution models with virtual particles at side chain centers. Example: CONS HMCM FORCE 50.0 WEIG REFX 10.4 REFY 12.1 REFZ 1.3 - SELECT RESID 21 .AND. .NOT. - ( TYPE H* .OR. TYPE N .OR. TYPE C .OR. TYPE O ) - END This will create a harmonic restraint with a force constant of 50 kcal/mol that holds the side chain center of mass at residue 21 of a protein near (10.4, 12.1, 1.3).

Fixing bond lengths or angles during dynamics. SHAKE is a method of fixing bond lengths and, optionally, bond angles during dynamics, minimization (not ABNR and Newton-Raphson methods), coordinate modification (COOR SHAKe command), and vibrational analysis (explore command). The method was brought to CHARMM by Wilfred Van Gunsteren (WFVG), and is referenced in J. Comp. Phys. 23:327 (1977). When hydrogens are present in a structure, it will allow a two-fold increase in the dynamics step size if SHAKE is used on the bonds. To use SHAKE, one specifies the SHAKE command before any SHAKE constraints usage. The SHAKE command has the following syntax: [SYNTAX SHAKe constraints] SHAKE { OFF } { shake-opt fast-opt 2x(atom-selection) [NOREset] } shake-opt:== [BONH] { [MAIN] } [TOL real] [MXITer integer] [BOND] { COMP } [ANGH] { PARAmeters } [SHKScale real] [ANGL] fast-opt:== { [ FAST [ WATEr water-resn ] ] } { NOFAst } BONH specifies that all bonds involving hydrogens are to be fixed. BOND specifies all bonds. ANGH specifies that all angles involving hydrogen must be fixed. ANGL specifies that all angles must be shaken. BOND is implied if any angles are fixed, otherwise, only the 1-3 distances would be fixed. Coordinates must be read in before the SHAKE command is issued, unless the PARAmeter option is specified. SHAKE constraints are applied only for atom pairs where one atom is in the first atom selection and one atom in the second atom selection. The default atom selection is ALL for both sets. TOL specifies the allowed relative deviations from the reference values (default: 10**-10). MXITer is the maximum number of iterations SHAKE tries before giving up (default: 500). When the SHAKE command is used, it will check that there are degrees of freedom available for all atoms to satisfy all their constraints. Angles cannot be fixed with SHAKE if one has explicit hydrogen arginines in the structure as the CZ carbon has too many constraints. This is a general problem for any structure which has too many branches close together. SHAKE is not recommended for fixing angles. The algorithm converges very slowly in the case where one has three angles centered on a tetravalent atom and the constraints are satisfiable only using out of plane motions. The use of SHAKE modifies the output of the dynamics command. The number appearing to the right of the step number is the number of iterations SHAKE required to satisfy all the constraints. This number should generally be small. When ST2's are present, SHAKE constraints are automatically applied for the O-H bonds and H-O-H angles. There is a PARAmeter option for the SHAKe command. This option causes the shake bond distances to be found from the parameter table rather than from the current set of coordinates. This option is NOT compatible with the use on angle SHAKE constraints, and it will give an error if this is tried. With these commands, the bond energy may be zeroed without any minimization with the command sequence; SHAKE BOND PARA COOR SHAKE [MASS] [SYNTAX SHAKe FAST constraints] SHAKe FAST [WATEr SELEct water_selection END] [OLDWatershake] [ MXITer <iterations> TOL <tolerance> ] [PARAmeter] [COMP] This command specifies the use of the new vector/parallel and analagous scalar fast SHAKE constraint routines (implemented Aug 2000). Certain assumptions are made when this command is issued: The only bonds involved are between heavy atoms and hydrogens, except for water molecules included in the WATEr selection ... end sub-command. This selection is used to indicate the water molecules that have an H-H bond. It is assumed that the selection will include all atoms in the water molecule and that said molecule contains exactly two X-H bonds and one H-H bond where X is any heavy atom. Testing for "hydrogen-ness" is done via the CHARMm hydrog() function which makes it's choice based on atomic mass. The prefered selection is through the use of the RESNAME selection specifier, eg: ... WATEr SELEct RESNAME TIP3 END By default, water molecules selected with the WATEr sub-command will be constrained via the use of a special water-SHAKE routine which uses the direct inversion method. This algorithm is from 25 to 30 % faster than the normal iterative, scalar SHAKE routine. For the rest of the heavy atom -hydrogen bonds, a vector/parallel version of the original SHAKE routine is used. This is about 5X the scalar SHAKE. If the optional keyword OLDWatershake is used, the vector/parallel (not the watershake) routines are used. The rest of the keywords are the same as in the original SHAKE command. Note: that FAST has to be the second word in command line.

[SYNTAX NOE constraints] NOE Invoke the module RESEt Reset all NOE restraint lists. This command clears all existing NOE restraints. Resets scale factor to 1.0 PNOE Turn on the restraint between a given atom specified by ASSIgn and a point specified by CNOX, CNOY and CNOZ intead of a restraint between two atoms. The use of this restraint is desirable for docking, and loop refinements. ASSIgn [KMIN real] [RMIN real] [KMAX real] [RMAX real] [FMAX real] [TCON real] [REXP real] {2X(atom_selection)} {[CNOX real] [CNOY real] [CNOZ real] 1X(atom selection) } Assign a restraining potential between the atoms the first selection and the atoms of the second selection. Where multiple atoms are selected, R = [ average( Rij**(1/REXP) ) ]**REXP where (i) runs over the first atom selection and (j) runs over the second atom selection. The default REXP value is 1.0 (a simple average). An REXP value of 3.0 may be optimal for NOE averaging. / 0.5*KMIN*(RAVE-RMIN)**2 R<RMIN / / 0.0 RMIN<R<RMAX E(R)= \ 0.5*KMAX*(RAVE-RMAX)**2 RMAX<RAVE<RLIM \ \ FMAX*(RAVE-(RLIM+RMAX)/2) RAVE>RLIM and RAVE=R TCON=0 RAVE=RRAVE**(-1/3) TCON>0 RRAVE=RRAVE*(1-DELTA/TCON)+R**(-3)*DELTA/TCON for initial conditions, RRAVE=RMAX**(-3) DELTA is the integration time step. For minimization, the value is either 0.001ps or the previous simulation value. Where: RLIM = RMAX+FMAX/KMAX (the value of RAVE where the force equals FMAX) Defaults for each entry: KMIN=0.0, RMIN=0.0, KMAX=0.0, RMAX=9999.0, FMAX=9999.0 TCON=0.0, REXP=1.0 Also, the old sytax is supported: ASSIgn rminvalue minvariance maxvariance 2X(atom_selection) For this format, KMAX=0.5*Kb*TEMP/(maxvariance**2) KMIN=0.5*Kb*TEMP/(minvariance**2) RMIN=rminvalue RMAX=rminvalue READ UNIT <integer> Reads restraint data structure from card file previously written. WRITe UNIT <integer> [ANAL] Writes out the restraint data in card format to a file on the specified unit. A CHARMM title should follow the command. SCALE are saved together with the lists in the NOE common block. The ANAL option will print out the distances and energy data computed with the current main coordinates. PRINT [ANAL [CUT real]] Same as the WRITe command except to the output file and slightly more user friendly form. A positive CUT value will list only those that have a distance that exceeds RMAX by more than DCUT. SCALe [real] Set the scale factor for the NOE energy and forces. Default value: 1.0 TEMPerature real Specify the temperature for the old format. END Return to main command parser. No other commands (I/O or loops) are supported inside the NOE module. Looping can be performed outside if necessary. The units are Kcal/mol/A/A for force constants and Angstroms for all distances. EXAMPLE. Set up some NOE restraints for one strand of a DNA-hexamer in a file to be streamed to from CHARMM. * SOME NOE RESTRAINTS FOR DNA. ASSUME PSF, COORD ETC ARE ALREADY PRESENT * ! First clear the lists NOE RESET END ! Since there are many identical atom pairs we use a loop set 1 1 label loop NOE ! Sugar protons, same in all six sugars (don't pay any attention to ! the numeric values) ASSIgn SELE ATOM A @1 H1' END SELE ATOM A @1 H2'' END - KMIN 1.0 RMIN 2.7 KMAX 1.0 RMAX 3.0 FMAX 2.0 ASSIgn SELE ATOM A @1 H3' END SELE ATOM A @1 H2'' END - KMIN 1.0 RMIN 2.7 KMAX 1.0 RMAX 3.0 FMAX 2.0 END incr 1 by 1 if 1 le 6 goto loop ! Now do some more specific things OPEN WRITE UNIT 10 CARD NAME NOE.DAT NOE SCALE 3.0 ! Multiply all energies and forces by 3 WRITE UNIT 10 * NOE RESTRAINT DATA FROM DOCUMENTATION EXAMPLE * PRINT ANAL ! See what we have so far PRINT ANAL CUT 2.0 ! list END RETURN

Apply general restrained distances allowing multiple distances to be specified. This restraint term has been added to allow for facile searching of a reaction coordinate, where the reaction coordinate is estimated to be a linear combination of several distances. By Bernard R. Brooks - NIH - March, 1995 [SYNTAX Restrained Distances] RESDistance [ RESEt ] [ SCALE real ] [ KVAL real RVAL real [EVAL integer] - [ POSItive ] [ IVAL integer ] repeat( real first-atom second-atom ) ] [ NEGAtive ] E = 1/EVAL * Kval * Dref**EVAL Where: Dref = K1*R1**Ival + K2*R2**Ival + ... + Kn*Rn**Ival - Rval Where K1,K2,...Kn are the real values in the repeat section and R1,R2,...Rn are the distances between specified pair of atoms. RESEt Reset the restraint lists. This command clears the existing restraints. Resets the scale factor to 1.0 SCALe real Set the scale factor for the energy and forces. Default value: 1.0 POSITIVE Include this restraint only when Dref is positive. NEGATIVE Include this restraint only when Dref is negative. If anything else is on the command line then a new restraint is added to the list of distance restraints. KVAL real The force harmonic constant RVAL real The target distance IVAL integer The exponent for individual distances. EVAL integer The exponent (default 2). EVAL must be positive. repeat( real first-atom second-atom ) The real value is a scale factor for the distance between the first and second specified atoms in the pair. EXAMPLES: 1. Create a reaction coordinate for QM/MM 2. Set up some restraints to force three atoms to make an equilateral triangle. !!! 1 !!! Create a reaction coordinate for QM/MM OPEN WRITE CARD UNIT 21 name reaction.energy OPEN WRITE FILE UNIT 22 name reaction.path TRAJECTORY IWRITE 22 NWRITE 1 NFILE 40 SKIP 1 * trajectory of a minimized reaction path * SET ATOM1 MAIN 11 OG SET ATOM2 MAIN 11 HG SET ATOM3 MAIN 23 OD1 SET 1 1 SET V -5.0 LABEL LOOP SKIP NONE ! make sure all energy terms are enabled RESDistance RESET KVAL 2000.0 RVAL @v - 1.0 @atom1 @atom2 -1.0 @atom2 @atom3 MINI ABNR NSTEP 200 NPRINT 10 PRINT RESDistances ! print a check of distances TRAJ WRITE ! write out the new minimized frame SKIP RESD ! turn off the restraint energy term ENERGY ! recompute the energy without restraints WRITE TITLE UNIT 21 ! write out the current restraint distance and energy * @V ?ENER * INCR 1 BY 1 ! increment the step counter INCR V BY 0.25 ! increment the restraint value IF 1 LT 40.5 GOTO LOOP RETURN !!! 2 !!! Make a water nearly an equilateral triangle set atom1 WAT 1 O set atom2 WAT 1 H1 set atom3 WAT 1 H2 RESDistance RESEt RESDistance KVAL 1000.0 RVAL 0.0 - 1.0 @atom1 @atom2 - 1.0 @atom1 @atom3 - -2.0 @atom2 @atom3 RESDistance KVAL 1000.0 RVAL 0.0 - 1.0 @atom1 @atom2 - -2.0 @atom1 @atom3 - 1.0 @atom2 @atom3 RESDistance KVAL 1000.0 RVAL 0.0 - -2.0 @atom1 @atom2 - 1.0 @atom1 @atom3 - 1.0 @atom2 @atom3 print resdistances mini abnr nstep 200 nprint 10 print resdistances stop !!! 3 !!! Prevent an atom from moving more than 20A from the others, ! but have no restraint energy when no distance is large. set atom1 SOLV 1 OH2 set atom2 SOLV 2 OH2 set atom3 SOLV 3 OH2 set atom4 SOLV 4 OH2 set atom5 SOLV 5 OH2 RESDistance RESEt RESDistance KVAL 1.5E-12 RVAL 6.4E7 IVAL 6 POSITIVE - 1.0 @atom1 @atom2 - 1.0 @atom1 @atom3 - 1.0 @atom1 @atom4 - 1.0 @atom1 @atom5 - 1.0 @atom2 @atom3 - 1.0 @atom2 @atom4 - 1.0 @atom2 @atom5 - 1.0 @atom3 @atom4 - 1.0 @atom3 @atom5 - 1.0 @atom4 @atom5 print resdistances mini abnr nstep 200 nprint 10 print resdistances stop

[SYNTAX External Forces] PULL { FORCe <real> } XDIR <real> YDIR <real> ZDIR <real> [PERIod <real>] { EFIEld <real> } { OFF } { LIST } [WEIGht] atom-selection A force will be applied in the specified direction on the selected atoms either as a constant: FORCe <value> specified in picoNewtons (pN) or oscillating in time: FORCe*COS(TWOPI*TIME/PERIod), FORCe <pN> PERIod <ps> time is counted from the start of the dynamcis run. The force due to an electrical EFIEld (V/m) (possibly also oscillating) may also be specified, in which case partial charges are taken from the psf and used to calculate the force. If WEIGht is specified the forces are multiplied by the wmain array. Each invocation of this command adds a set of forces to the previously defined set. PULL OFF turns off all these forces. PULL LIST produces a listing. NB! Forces defined by PULL will move atoms in the specified direction, which is opposite to that listed by the forces from the COOR FORCE command.

The RMSD restraint is useful to manipulate and control macromolecular conformations. The restraint is related to the CONS HARM BestFit, which sets up harmonic restraints with respect of a reference structure. However, because all the reference data structure is stored in XREF, YREF, ZREF, this command allows only a single bestfit restraint. In addition, it allows only a restraint to zero value of RMSD. It is useful to allow multiple such bestfit RMSD restraint to progress from one conformation to a second conformation of a molecular system. The new command CONS RMSD allows such multiple bestfit restraint. In fact, that is principally the advantage over the BESTfit method (only the data structure is changed, the energy subroutines themselves are the same). The method can also be used to performed targetted trajectories. The form of the new restraint energy is: E = Sum_i KFORCE_i * [RMSD - OFFSET_i]**2 Where RMSD is the (possibly mass-weighted) root-mean-square-deviation (RMSD) of the current coordinates with respect to a reference structure, KFORCE_i is a force constant, and OFFSET_i is a constant value setting a relative distance with respect to the RMSD of the structure. The restraint energy is equivalent the normal BestFit energy. The forces have been checked with the TEST FIRST command. All the data structure is stored dynamically on the HEAP and thus, no extra permanent (static) storage is introduced. The size of initial HEAP storage is set by the MAXRmsd integer the first time that the command is issued (by default this is set to the number of atoms if nothing is specified). By specifying the RELATIVE keyword, it is possible to impose a 1-D constraint to simultaneously constrain a given structure with respect to two end-point structures. This is achieved by constraining the difference (RMSD2 - RMSD1) instead of just the RMSD1 or RMSD2 values individually, where RMSD1 and RMSD2 are the RMSD values of given structure from endpoint structure 1 and 2 respectively. This allow full freedom of movements orthogonal to the relative axis. For the relative RMSD constraint, the form of the new restraint energy is: E = Sum_i KFORCE_i * [(RMSD2-RMSD1) - OFFSET_i]**2 The syntax is very similar to all current restraints in CHARMM: CONS RMSD {RELAtive} {MAXRmsd integer} orient-specs force-const-spec - coordinate-spec atom-selection CONS RMSD SHOW CONS RMSD CLEAR force-const-spec ::= { FORCE real } [MASS] {OFFSet real} orient-specs ::= [ NOROtation ] [ NOTRanslation ] coordinate-spec::= { [MAIN] } { COMP } CONS CLEAR removes all multiple RMSD restraints CONS RMSD SHOW prints all current RMSD restraints with all parameters.

[SYNTAX Rg/RMSD resteaint] RGYRation { FORCe <real> } REFErence <real> [RMSD] [COMParison] [ORIEnt] OUTPut_unit <integer> NSAVe_output <integer> SELEction <atom selection> END { RESEt } This restraint force restraints the central moment of the selected atoms about 1) the center of geometry of the selected atoms (Rg restraint) or 2) a specified reference structure structure (RMSD). The form of the restraint term is: 0 2 E= 1/2 * CONST * (R - R ) GY GY where 2 2 R = 1/N SUM ( r - R ) (Rg restraint) GY i i CG and R = 1/N SUM ( r ) CG i i or 2 ref 2 R = 1/N SUM ( r - R ) (RMSD restraint) GY i i i The specific terms are: RGYR - Invoke the Rg/RMSD restraint term parser in CHARMM FORCe <real> - Use a restraint force constant (CONST above) of <real> kcal/mol/A^2 REFErence <real> - Use a target Rg/RMSD value of <real>, in A. RMSD - Employ RMSD based restraint instead of Rg restraint. COMP - Use comparison cordinate set as reference (default uses main). ORIEnt - Do a coor orie on coordinates before computing RMSD. OUTPut <integer> - During dynamics write Rg/RMSD history to unit <integer>. NSAVe <integer> - Save Rg/RMSD history every <integer> steps. RESEt - CLear Rg/RMSD restraint flags, release memory. Usage: The following examples illustrate the use of this restraint term. 1) Add an Rg restraint potential to dynamics run, save trajectory information to unit. Base Rg calculation on Ca positions only. open unit 12 write form name traj.rgd RGYRestraint Force 50 Reference 12.9 - output 12 nsave 50 select type ca end 2) Add an RMSD based restraint to target a conformational change in a loop. open unit 1 read form name open.crd read coor card unit 1 close unit 1 open unit 1 read form name closed.crd read coor card compare unit 1 close unit 1 coor orie rms select type ca end coor rms select ( ires 12:24 .and. .not. hydrogen ) end Calc drms = ?rms / 6 Calc rmsd = ?rms - @drms set count 1 label domini rgyr force 50 reference @rmsd rmsd comp - select ( ires 12:24 .and. .not. hydrogen ) end mini conj nstep 400 tolenr 0.00001 cutnb 12 ctofnb 10 ctonnb 8 - inbfrq -1 atom cdie vatom vswitch fshift bycb rgyr reset coor rms select ( ires 12:24 .and. .not. hydrogen ) end open unit 1 write form name o2c_@count.pdb write coor pdb unit 1 * Coordinates from frame @count of open to closed path. * Current loop rmsd (residues 12-24 ca only) is ?rms A. * incr count by 1 Calc rmsd = @rmsd - @drms if rmsd gt 0.1 goto domini 3) Use RMSD restraint to unfold a helical peptide with RMSD computed based minimum RMSD at each step (Oriented). set rmsd 2 label unfold rgyr force 100 reference @rmsd rmsd comp orient select type ca end mini conj nstep 400 tolenr 0.00001 rgyr reset coor orie rms select type ca end open unit 1 write form name frame@rmsd.pdb write coor pdb unit 1 * Coordiantes from frame with reference rmsd = @rmsd, current rmsd= ?rms * incr rmsd by 2 if rmsd le 10 goto unfold __________________________________________________________________________

[SYNTAX Distance Matrix restraint] DMCOnstrain FORCe real REFErence real OUTPut_unit integer NSAVe_output integer CUTOff real NCONtact integer {SELE {atom selection} WEIGt real}(ncontact times) THIS COMMAND ADDS A Quadratic POTENTIAL to restrain the reaction coordinate. The reaction coordinate is defined as a weighted sum of contacts. 2 E= 1/2 * CONST * (RHO - DMC0) where RHO = SUM (Weigt * (1-STATE ); i i i 1 STATE = ---------------------------- i 1 + EXP(20*(DIST - (CUTOff+0.25))) i DIST - distance between centers of geometry of residues i forming contact i Usage: The following examples illustrate the use of this restraint term. 1) Add an distance matrix restraint potential to dynamics run, save trajectory information to unit. This example applies a distance restraint of the form given above between pairs of side chain centers-of-mass for a set of 54 contacts and restrains the system to a fractional value of the overall reaction coordinate of 0.625. Each restraint term is given a weight based on the amount of time the given contact was formed in the native state simulation. For details of the method used here, the reader is referred to: [Sheinerman and Brooks, JMB, 278, 439 (1998).] open unit 25 write form name "dmc/GB1H.rho" define bb - sele segid agb1 .and. - (type ca .or. type c .or. type n .or. type o ) end define sd - sele segid agb1 .and. .not. (bb .or. hydrogen) end set dmforce 2000. set dmref 0.625 set dmsave 100 DMCO FORCe @dmforce REFE @dmref OUTPut 25 NSAVe @dmsave - CUTOff 6.5 NCONtact 54 sele sd .and. (resi 2 .or. resi 4 ) end WEIGht 0.8158139980007818 sele sd .and. (resi 4 .or. resi 21 ) end WEIGht 0.9665094391591674 sele sd .and. (resi 4 .or. resi 24 ) end WEIGht 0.9879192119842544 sele sd .and. (resi 4 .or. resi 27 ) end WEIGht 0.9895819946415852 sele sd .and. (resi 4 .or. resi 51 ) end WEIGht 0.9408263780596178 sele sd .and. (resi 5 .or. resi 18 ) end WEIGht 0.9415959785662404 sele sd .and. (resi 6 .or. resi 8 ) end WEIGht 0.9999909781703169 sele sd .and. (resi 6 .or. resi 17 ) end WEIGht 0.9995401666453647 sele sd .and. (resi 6 .or. resi 31 ) end WEIGht 0.9999999999999796 sele sd .and. (resi 7 .or. resi 16 ) end WEIGht 0.9796513289404690 sele sd .and. (resi 7 .or. resi 52 ) end WEIGht 0.7780795300785477 sele sd .and. (resi 7 .or. resi 54 ) end WEIGht 0.6905994027412474 sele sd .and. (resi 8 .or. resi 17 ) end WEIGht 0.8323463051907218 sele sd .and. (resi 8 .or. resi 35 ) end WEIGht 0.9731361885884368 sele sd .and. (resi 8 .or. resi 38 ) end WEIGht 0.9174238684004473 sele sd .and. (resi 8 .or. resi 40 ) end WEIGht 0.9754236727233426 sele sd .and. (resi 8 .or. resi 55 ) end WEIGht 0.9151151195555089 sele sd .and. (resi 9 .or. resi 14 ) end WEIGht 0.6645390074837504 sele sd .and. (resi 9 .or. resi 56 ) end WEIGht 0.7285333256999120 sele sd .and. (resi 17 .or. resi 19 ) end WEIGht 0.8912444191627017 sele sd .and. (resi 17 .or. resi 34 ) end WEIGht 0.8920438869599703 sele sd .and. (resi 19 .or. resi 21 ) end WEIGht 0.7259406753340431 sele sd .and. (resi 19 .or. resi 30 ) end WEIGht 0.6711322572172727 sele sd .and. (resi 19 .or. resi 34 ) end WEIGht 0.7844587325555364 sele sd .and. (resi 21 .or. resi 27 ) end WEIGht 0.9999999531742481 sele sd .and. (resi 23 .or. resi 25 ) end WEIGht 0.9999999994693732 sele sd .and. (resi 23 .or. resi 26 ) end WEIGht 0.9999999999991671 sele sd .and. (resi 24 .or. resi 27 ) end WEIGht 0.9979691873576392 sele sd .and. (resi 24 .or. resi 51 ) end WEIGht 0.6964187937040895 sele sd .and. (resi 25 .or. resi 28 ) end WEIGht 0.8927269972864454 sele sd .and. (resi 25 .or. resi 29 ) end WEIGht 0.8210307146883757 sele sd .and. (resi 26 .or. resi 29 ) end WEIGht 0.8905543107011445 sele sd .and. (resi 27 .or. resi 30 ) end WEIGht 0.9612292542758489 sele sd .and. (resi 27 .or. resi 31 ) end WEIGht 0.9999999983165117 sele sd .and. (resi 28 .or. resi 53 ) end WEIGht 0.9290808245024628 sele sd .and. (resi 30 .or. resi 33 ) end WEIGht 0.9273633852785603 sele sd .and. (resi 30 .or. resi 34 ) end WEIGht 0.9852961901326586 sele sd .and. (resi 31 .or. resi 53 ) end WEIGht 0.9960510555412353 sele sd .and. (resi 32 .or. resi 44 ) end WEIGht 0.9811553525890055 sele sd .and. (resi 35 .or. resi 40 ) end WEIGht 0.9996382371796980 sele sd .and. (resi 35 .or. resi 44 ) end WEIGht 0.9529057898756480 sele sd .and. (resi 35 .or. resi 55 ) end WEIGht 0.9921250365257495 sele sd .and. (resi 38 .or. resi 40 ) end WEIGht 0.9469272633832431 sele sd .and. (resi 40 .or. resi 55 ) end WEIGht 0.9855702226874301 sele sd .and. (resi 40 .or. resi 57 ) end WEIGht 0.7830957174831968 sele sd .and. (resi 44 .or. resi 55 ) end WEIGht 0.9999950887381377 sele sd .and. (resi 45 .or. resi 54 ) end WEIGht 0.9994979068986675 sele sd .and. (resi 47 .or. resi 49 ) end WEIGht 0.9878049213251836 sele sd .and. (resi 47 .or. resi 50 ) end WEIGht 0.9999916748639699 sele sd .and. (resi 47 .or. resi 52 ) end WEIGht 0.9881469299868514 sele sd .and. (resi 50 .or. resi 52 ) end WEIGht 0.9973918765679025 sele sd .and. (resi 51 .or. resi 53 ) end WEIGht 0.8168211946297691 sele sd .and. (resi 52 .or. resi 54 ) end WEIGht 0.8871232193909784 sele sd .and. (resi 54 .or. resi 56 ) end WEIGht 0.8700639041799975 __________________________________________________________________________

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NIH/DCRT/Laboratory for Structural Biology

FDA/CBER/OVRR Biophysics Laboratory

Modified, updated and generalized by C.L. Brooks, III

The Scripps Research Institute