CHARMM c39b2 cons.doc
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
* Puckering:: "CONS PUCK" Hold puckering 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:: "CONS RMSD" Holds atoms in place relative to
reference structure/structures
* EMAP restraints:: "CONS EMAP" Soft restraint to induce a group of atoms
to a shape defined by structures or maps
* 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
* COFM along path:: "CONS PATH" Constrain center of mass along 3D path
* Helix Restraint:: "CONS HELI" Impose helix 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.
WIDTh is specified in degrees.
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 puckering coordinates near selected values
Using this form of the CONS command, one may put restraints on
the puckering coordinates formed by sets of any six atoms. Harmonic potential
is used to for the restraint.
The command for setting the puckering restraints is as follows:
Syntax:
[SYNTAX CONS PUCKering]
CONS PUCKering 6-atom-spec restraint-spec [output-spec]
6-atom-spec::= { [ BYNUM 6x(int) ] }
{ [ atom-selection ]}
{ [ 6X(atom-spec) ] }
restraint-spec::= [ KCONst 3x(real) ] [ VALUe 3x(real) ] [ EXPOnent 3x(real) ]
output-spec:== [OUTUnit integer] [PKFRQ integer]
CONS CLPC
Syntactic ordering:
* PUCK or CLPC must directly follow CONS (must be the next word),
* atom selection or spec must directly follow PUCK (must next information after PUCK),
* KCONst, VALUe and EXPOnent must follow selection or spec of atoms
Arguments and options:
----------------------
Keyword Default Purpose
BYNYM none Specify 6 atoms as numbered in the psf for the pucker as 6 integers
atom-selection none Use atom selection to select 6 atoms
6X(atom-spec) none Use atom-specs six times to specify atoms
KCONst 0.0 0.0 0.0 Force constants for restraints on Q, theta, phi
VALUe 0.0 0.0 0.0 Potential minimum location for restraints on Q, theta, phi
EXPOnent 0.0 0.0 0.0 Exponents on harmonic potential for Q, theta, phi
Output:
-------
During dynamics only, the output of the value of Q, theta, and phi
for each restraint applied are written to the output unit at the specified frequency
(PKFRQ) in the following ascii format
step-number Q1 theta1 phi1 Q2 theta2 phi2 ...
Example output for two pucker constraints, 20 steps, pkfrq=10:
10 2.161181 0.707060 2.306795 0.375264 0.799902 3.412435
20 2.287641 0.610042 2.177232 0.531637 0.182914 3.255958
Functional form
---------------
PUCKering adds harmonic restraint to the puckering coordinates of the
selected six atoms. The puckering coordinates are given by Q, theta, and phi as
defined by Cremer & Pople, see: D. Cremer and J. A. Pople,
JACS 97:6, page 1354, 1975. NCSU variable is set that is equal to the total
number of puckering restraints.
The restraining potential energy is given by
Epuck = EQ + Etheta + Ephi
where EQ, Etheta, and Ephi are potentials given by
EQ = KCON(1)*(Q - VALU(1))**EXPO(1)
Etheta = KCON(2)*(theta - VALU(2))**EXPO(2)
Ephi = KCON(3)*(phi - VALU(3))**EXPO(3)
CLPC clears the list of restrained puckering coordinates.
Other commands:
--------------
The PRINT CONS command, see *note print:(io.doc)print,
will work for restraints.
QUICK command can be used to calculate the puckering coordinates,
see *note print:(miscom.doc)
CORREL command has an ENTER option to calculat pucker
Examples:
---------
1) Specifying atoms by the atom-spec method, specifies a quadratic harmonic potential
on Q, theta, and phi centered on 0.6, 0.2, and 3.3, respectively, and with force
constants all 10 kcal/mol/Angstrom**2. Output of the values of Q, theta, and phi
will be written to unit 21 every 10 steps.
cons puck sugar 1 o5 sugar 1 c1 sugar 1 c2 sugar 1 c3 sugar 1 c4 sugar 1 c5 -
kcon 10.0 10.0 10.0 valu 0.6 0.2 3.3 expo 2.0 2.0 2.0 outu 21 pkfrq 10
1) Specifying atoms by the BYNUM method, otherwise same as above except there will be
no pucker output during dynamics.
cons puck bynum 7 1 8 12 16 5 kcon 10.0 10.0 10.0 valu 0.6 0.2 3.3 expo 2.0 2.0 2.0
-----------------------------------------------------------------------------
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 RDISt real [WEIGhting or MASS]
reference-spec atom-selection
where:
reference-spec ::= [REFX real] [REFY real] [REFZ real]
at least one must be specified.
This command will harmonically restrain centers of mass from
the selected atoms to the absolute reference point specified with
REFX, REFY and REFZ, or to a line specifying REFX, REFY or REFZ, or to
a plane specifying any two of REFX, REFY, and REFZ. The force constant
of the harmonic potential is set with the FORCe keyword. A reference
distance can be given with RDISt (default: ZERO). 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 1:
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).
Example 2:
cons hmcm force 100.0 mass refx 10.0 -
select segid ligand end
This will create a harmonic restraint with a force constant of
100 kcal/mol that keeps the center of mass of segment "ligand" on a
line with x value 10.0 but no restraints on the y or z values.
File: Cons -=- Node: SHAKE
Up: Top -=- Next: NOE -=- Previous: Center of Mass
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 water-resn] [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 specified by the
WATEr water-resn 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.
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. CAVE: PNOE itself is NOT a
command -- the PNOE feature is invoked implicitely by
the presence of the CNOX, CNOY, CNOZ point specification.
ASSIgn [KMIN real] [RMIN real] [KMAX real] [RMAX real] [FMAX real]
{MINDIST} {RSWI real [SEXP real]} {SUMR}
[TCON real] [REXP real] {2X(atom_selection)}
{[CNOX real] [CNOY real] [CNOZ real] 1X(atom selection) }
Assign a restraining potential between the atoms of 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.
If SUMR keyword is present, R is computed as following,
R = [ Sum_ij ( Rij**(1/REXP) ) ]**REXP
In this case, REXP=-1/6 might be typically used.
If the key work MINDIST is specified, then the NOE constraint
will be active only between the pair of atoms from the two selected
set of atoms that happend to be the nearest at all time during
the dynamics (useful to resolve ambiguous distance restraints).
/ 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
If RSWItch is specified, a soft-square NOE potential will be used,
where the square-well function is used for distances within a
specified "switching" region (specified by the RSWItch keyword),
whereas outside this region a "soft" asymptote is used:
/ 0.5*KMIN*(RAVE-RMIN)**2 R<=RMIN
E(NOE)= 0.0 RMIN<R< RMAX
\ 0.5*KMAX*(RAVE-RMAX)**2 RMAX<R<=RMAX+RSWITCH
\ A+B/(RAVE-RMAX)**SEXP+FMAX*(RAVE-RMAX) R> RMAX+RSWITCH
where,
A,B are determined such that both E and force are continuous.
FMAX defines the final asymptote slope (default 1.0)
RSWI defines the switching start point (default 1.0)
SEXP exponent of the soft asymptote (default 1.0)
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
MPNOe INOE <integer> {[TNOX real] [TNOY real] [TNOZ real]}
Define INOE as a moving point-NOE with target position
TNOX, TNOY, TNOZ -- the initial position is that given
in the previous assign statement of the NOE (CNOX...).
NMPNoe <integer>
No of steps over which the point-NOE's are moved from
their initial points (CNOX...) to the target points (TNOX...).
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
EXAMPLE2. Set up some NOE restraints with soft asymptote (protein G)
...
if @?rexp eq 0 set rexp = -0.166666666666667
if @?kmin eq 0 set kmin = 1
if @?kmax eq 0 set kmax = 1
if @?fmax eq 0 set fmax = 1
if @?rswi eq 0 set rswi = 3
if @?sexp eq 0 set sexp = 1
NOE
RESET
ASSI rmin 1.8 rmax 5.5 -
SELE resid 39 .AND. type HG1# end SELE resid 34 .AND. type HB# end -
rexp @rexp fmax @fmax rswi @rswi sexp @sexp kmin @kmin kmax @kmax SUMR
ASSI rmin 1.8 rmax 6.5 -
SELE resid 39 .AND. type HG2# end SELE resid 34 .AND. type HB# end -
rexp @rexp fmax @fmax rswi @rswi sexp @sexp kmin @kmin kmax @kmax SUMR
ASSI rmin 1.8 rmax 5 -
SELE resid 34 .AND. type HA end SELE resid 39 .AND. type HN end -
rexp @rexp fmax @fmax rswi @rswi sexp @sexp kmin @kmin kmax @kmax SUMR
PRINT ANAL
END
EXAMPLE3. Set up moving point-NOE restraints for docking of a ligand
...
NOE
RESET
assign kmax 10.0 rmax 2.0 fmax 10.0 -
CNOX -7.899 CNOY 40.864 CNOZ 50.967 -
sele atom LGND 1 H27 end
assign kmax 10.0 rmax 2.0 fmax 10.0 -
CNOX -10.033 CNOY 38.295 CNOZ 50.258 -
sele atom LGND 1 N16 end
assign kmax 10.0 rmax 2.0 fmax 10.0 -
CNOX -11.621 CNOY 36.654 CNOZ 48.924 -
sele atom LGND 1 H28 end
assign kmax 10.0 rmax 2.0 fmax 10.0 -
CNOX -17.948 CNOY 39.618 CNOZ 60.275 -
sele atom LGND 1 H42 end
print anal
NMPNoe 40000
MPNOe INOE 1 -
TNOX 13.177 TNOY 45.357 TNOZ 49.337
MPNOe INOE 2 -
TNOX 11.043 TNOY 42.788 TNOZ 48.628
MPNOe INOE 3 -
TNOX 9.455 TNOY 41.146 TNOZ 47.294
MPNOe INOE 4 -
TNOX 3.128 TNOY 44.111 TNOZ 58.645
END
...
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> }
[SWITch <int>] [SFORce <real>]
[WEIGht] [atom-selection]
{ TORQue <real> } [PERIod <real>]
[AXIS | XDIR <real> YDIR <real> ZDIR <real> -
XORI <real> YORI <real> ZORI <real>]
{ OFF }
{ LIST }
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.
or forces due to an electrical EFIEld (V/m) (possibly also oscillating).
Partial charges are then taken from the PSF and used to calculate the force.
If WEIGht is specified the forces are multiplied by the wmain array.
The invocation of a non-zero SWITch value will result in a linearly
time-varying force. This command must be used in conjunction with a
dynamics routine (using leap-frog integrator). The force is switched
linearly between SFORce <pN> (starting force) and FORCe <pN> (end force)
over the course of the simulation.
TORQue <pN/A> either uses the axis defined by a prior COOR AXIS command
(or any COOR command which sets the corman axis) or an axis has to be
specified with the *DIR and *ORI keywords.
Torque code fromi J Wereszczynski & I Andricioae: PNAS (2006)103:16200
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
Additionally to the RMSD RELAtive option, a HPLAne keyword can be
specified, which switch to the formula:
E_hp = Sum_i KFORCE_i * [(RMSD2**2-RMSD1**2) - OFFSET_i]**2
and creates a constraints within hyperplanes rather than hyper-hyperbolas.
As a consequence iso-potential surfaces are equidistant and should not
introduce a bias towards conformations away from the ref1 - ref2 axis.
Note that this formula looks quartic, but is in fact quadratic due to
elimination of quadratic terms in the inner parenthesis. The NORM
keyword divides RMSD1, RMSD2 and OFFSET by 2.dist(Ref1-Ref2)=2.R_1,2
so that E_hp is effectively:
E_hp = Sum_i KFORCE_i * [ (R-R_m).N - OFFSET_i/(2.R_1,2)]**2
where R is the current position, R_m=(Ref2+Ref1)/2 is the midpoint
between Ref1 and Ref2, and N=(Ref2-Ref1)/|Ref2-Ref1|, the normalized
vector between Ref1 and Ref2.
The syntax is very similar to all current restraints in CHARMM:
CONS RMSD { RELAtive [HPLAne [NORM]] } {MAXN integer} {NPRT} orient-specs -
force-const-spec coordinate-spec atom-selection
CONS RMSD SHOW
CONS RMSD CLEAR
orient-specs ::= [ NOROtation ] [ NOTRanslation ]
force-const-spec ::= { FORCE real } [MASS] {OFFSet real} { BOFFset real}
coordinate-spec::= { [MAIN] }
{ COMP }
CONS CLEAR
removes all multiple RMSD restraints
CONS RMSD SHOW
prints all current RMSD restraints with all parameters.
The specific terms are:
RELAtive - Employ relative RMSD restraint using two reference
structures as defined above
HPLAne - With RELAtive, use hyperplane formula (see above).
NORM - With RELAtive HPLAne normalize the formula (see above).
NPRT - This suppresses the printout of the RMSD to URMSD
unit in a dynamics simulation. The default is to print
all RMSD.
MAXN - Maximum number of RMSD restraints (replaces MAXRMSD
used in previous versions) default setting = 10
COMP - Use comparison cordinate set as reference
(default uses main).
FORCE <real> - Force constant for RMSD term in kcal/mol/A^2
OFFSet <real> - RMSD value in A^ at which the structure is restrained
BOFFset <real> - offset at which to begin applying the harmonic RMSD
restraint, useful in specifying a flat-bottom RMSD
potential around the reference structure
IMPORTANT NOTES:
1. The MAXRMSD variable specifying total number of restrained atoms used
before has been replaced by the variable MAXN specifying the number of
RMSD restraints. This allows dynamic allocation of memory for storing
reference structures during atom selection for the RMSD restraint, which
reduces memory usage significantly
2. The c32 release contained additions including the ZETA potential and
the ability to fit one set of atoms using RMSD and apply the forces to
another set of atoms. These are not included in the present version due
to their inability to pass TEST FIRST
3. RMSD restraints can be used with DYNAmics command.
DYNAmics ... [ RMSD URMSD integer ] This will cause the RMSD values
for each of the RMSD restraints to be written to the unit specified by URMSD,
unless the NPRT option is pecified when the RMSD restraint is defined.
-------------------------------------------------------------------------
The EMAP restraint is useful to maintain a selection of atom to given shapes.
The restraint is related to the EMAP functions that use map objects for energy
calculation and simulation. A restraint map is either generated from a selection
of atoms, or an existing map object defined with EMAP, or readin from an external
file. An EMAP restraint is non-invasive or non-restricted and permit restrained atoms
to be far away from their restrained positions. Therefore, EMAP restraints can be
used to bias certain conformations or to induce a simulation system to change to
desired conformations, which we term as "targeted conformational search" (see reference:
Wu, X., Subramaniam, S., Case, D.A., Wu, K. W., Brooks, B.R., "Targeted
conformational search with map-restrained self-guided Langevin dynamics:
application to flexible fitting into electron microscopic density maps",
J Struct. Biol., 183, 429-440 (2013)).
The form of the EMAP restraint energy is:
E = KEMAP * Sum_i [AMASS_i * MAP_Norm_at_i]
Where KEMAP is the restraint constant, kcal/g, AMASS_i is atomic mass of atom i, g/mol.
MAP_Norm_i is the normalized vaule of the restraint map at atom i, which is interpolated
with b-spline.
The atom-selection defines the atoms to be restrained. The map definition defines
the restraint map. The map can be either generated from the coordinates of the selected
atoms, either in the main or the comparison set, or using existing map objects, or read
in from a map file. The restraint map object is fixed in space by default. A keyword,
MOVE, will make the restraint map movable during simulation.
The syntax is :
CONS EMAP FORCe real {atom-selection map-definition [MOVE]}
CONS EMAP SHOW
CONS EMAP [RESEt|CLEAR]
map-definition ::= {MAPId string }
{FILEname string }
{[DX real][DY real][DZ real][RESO real][COMP]}
CONS EMAP CLEAR
removes all EMAP restraints defined with CONS EMAP
CONS EMAP SHOW
prints all current EMAP restraints with all parameters, including those defined with EMAP CONS (See emap.doc).
The specific terms are:
FORCE <real> - Force constant for EMAP restraint in kcal/g
DX,DY,DZ <real> - grid size of generated map in x, y, and z directions,
Default: 3 angstroms.
RESOlution <real> - Resolution of the generated map. Default: 3 angstroms.
RIGId <string> Rigid ID define with EMAP commands. Using
MAPId <string> MAP ID define with EMAP commands. Using a map object
FILEname <string> A map filename in either .map, .ccp4, or .mrc format.
MOVE A flag to make the restraint map movable.
-------------------------------------------------------------------------
[SYNTAX Rg/RMSD restraint]
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
__________________________________________________________________________
[SYNTAX CONS PATH]
Syntax: CONS PATH spline-pts [COMP] [TEST unit]
FORCe real TZERo real atom-selection
:
:
:
FORCe real TZERo real atom-selection
CONS PATH CLEAR
CONS PATH POST
where:
spline-pts ::= { SPLUnit unit }
{ SPLIne atom-selection }
This command will harmonically restrain the projections of centers
of mass onto an arbitrary three-dimensional path. The path is specified with
cubic splines. Essentially, this is achieved by first projecting each
center of mass (COM) onto a cubic spline interpolated path to establish
an initial projection position (TINI). Then a restraint is applied to
the COM with respect to its TINI. For N spline points,
1.0 <= TINI <= N
where, for example, if TINI = 3.48 then the COM is projected onto
the spline piece between spline point 3 and spline point 4 while the digits
to the right of the decimal place corresponds to the cubic spline parameter
that gives the X, Y, Z coordinates that lie on spline piece 3.
The initial reference coordinates (used for determining TINI) can
be the current set (default) or a comparison set (COMP keyword).
The spline-pts are selected either from an atom selection if
SPLIne is given or read from a previously opened unit given
with the SPLUnit keyword. By default, the spline-pts are taken from the
main set. If the COMP key is specified in the absence of the SPLUnit
keyword then the spline-pts are taken from the COMP set. However,
if both the COMP and SPLUnit keys are used then the spline-pts are
taken from the coordinates that are read from the external file. Thus,
it is possible to define the initial coordinates separately from the
spline points by using the COMP key along with SPLUnit.
The reference point (relative to TINI) is specified by TZERo
and is recommended to have a value that is near TINI (usually,
within 1.0 of TINI). A negative TZERo value specifies a reference point
to the "left" of TINI while a positive TZERo value speficies a reference
point to the "right" of TINI.
The restraint force constant can be set to any positive
value (specified by the FORCE keyword followed by the desired value).
Multiple centers of mass can be defined for a given path by repeating
the FORCe, TZERo, and atom-selection.
The functional form of the restraint potential is:
2
U(T) = FORCE * [ (T - TINI) - TZERO ]
where T is the instantaneous projection onto the spline of a given
center of mass.
The spline interpolation (derived from user defined spline points)
and COM projections can be visualized by specifying the TEST key followed
immediately by a user defined output unit. The output data structure
is shown in Example 4 below.
Using CONS PATH POST will output infornation to OUTU. This is
convenient when used in conjunction with analyzeCHARMM.pl (MMTSB Toolset).
The output takes on the form:
PATH = 1 COM = 1 TINIT = 1.36523799 TZERO = -0.10000000 ABSTZERO = 1.26523799 TPRIME = 1.26773721
Each COM is written while specifying which path the COM corresponds with,
the COM number, the initial T-value from the first simulation window,
the relative TZERO (relative to the initial T-value), the absolute TZERO,
and TPRIME (the COM projection onto the path).
The primary use of this command is to restrain the movement of
a specific center of mass parallel to a user defined path. For instance,
DNA can be restrained to translocate along its phosphate backbone while
resembling a screwing motion.
Example 1:
CONS PATH SPLINE SELECT TYPE P .AND. SEGID N01F END -
FORCE 5 TZERO 0.35 SELECT SEGID N01F .AND. RESID 18 END -
FORCE 5 TZERO 0.35 SELECT SEGID N01F .AND. RESID 19 END -
FORCE 5 TZERO 0.35 SELECT SEGID N01F .AND. RESID 20 END
This will use the phosphorous atoms to generate a cubic spline.
Then it will create a harmonic restraint with a force constant of
5 kcal/mol that holds the centers of mass at residues 18, 19, and 20 to
its corresponding TINI+0.35 position.
Example 2:
CONS PATH COMP SPLINE SELECT TYPE P .AND. SEGID N01F END -
FORCE 2 TZERO 0.27 SELECT SEGID N01E .AND. RESID 5 END -
FORCE 2 TZERO 0.27 SELECT SEGID N01E .AND. RESID 6 END -
FORCE 2 TZERO 0.27 SELECT SEGID N01E .AND. RESID 7 END
This will use the phosphorous atoms to generate a cubic spline.
Then it will create a harmonic restraint with a force constant of
2 kcal/mol that holds the centers of mass at residues 5, 6, and 7 to
its corresponding TINI+0.27 position. However, TINI is determined from
the comparison set and not the default main set. Note that COM at
residues 5-7 from segid N01E are restrained with respect to the
phosphorus atoms of segid N01F (and not segid N01E).
Example 3:
OPEN UNIT 77 READ FORM NAME "SPLINE.PTS"
CONS PATH COMP SPLUNIT 77 -
FORCE 10 TZERO -0.5 SELECT SEGID N01E .AND. RESID 8 END -
FORCE 10 TZERO -0.5 SELECT SEGID N01E .AND. RESID 9 END -
FORCE 10 TZERO -0.5 SELECT SEGID N01E .AND. RESID 10 END
This will use the coordinates contained in the file "SPLINE.PTS"
(and not from the comparison set) to generate a cubic spline. The name of
the file containing the spline points is irrelevant but the format must be
arranged as follows:
-48.847 75.201 8.114
-68.551 73.231 9.000
-55.690 77.369 8.591
48.049 74.225 10.388
Then it will create a harmonic restraint with a force constant of
10 kcal/mol that holds the centers of mass at residues 8, 9, and 10 to
its corresponding TINI+(-0.5) position. However, TINI is determined
from the comparison set and not the default main set.
Example 4:
OPEN UNIT 88 WRITE FORM NAME "VISUALIZE.PDB"
CONS PATH TEST 88 SPLINE SELECT TYPE P .AND. SEGID N01F END -
FORCE 1 TZERO -0.19 SELECT SEGID N01F .AND. RESID 14 END -
FORCE 1 TZERO -0.19 SELECT SEGID N01F .AND. RESID 12 END -
FORCE 1 TZERO -0.19 SELECT SEGID N01F .AND. RESID 13 END
This will use the phosphorous atoms to generate a cubic spline.
Then it will create a harmonic restraint with a force constant of
1.0 kcal/mol that holds the centers of mass at residues 14, 12, and 13 to
its corresponding TINI+(-0.19) position. Furthermore, the spline interpolation
and COM projections can be visualized from the file "VISUALIZE.PDB" where
the contents of the file are arranged as follows:
ATOM 1 P 1 S 1 20.356 13.969 16.245 1 0.000
ATOM 2 O1P 1 S 1 18.599 13.199 16.040 1 0.271
ATOM 3 O2P 1 S 1 17.720 12.850 15.920 1 0.407
ATOM 4 O5* 1 S 1 16.840 12.543 15.780 1 0.543
ATOM 5 C5* 1 S 1 15.959 12.292 15.612 1 0.679
ATOM 6 C4* 1 S 1 15.076 12.112 15.409 1 0.814
ATOM 7 C3* 1 S 1 14.192 12.017 15.165 1 0.950
ATOM 8 P 2 S 2 13.866 12.006 15.063 2 0.000
ATOM 9 O1P 2 S 2 12.107 12.179 14.397 2 0.271
ATOM 10 O2P 2 S 2 11.254 12.395 14.000 2 0.407
ATOM 11 O5* 2 S 2 10.435 12.684 13.567 2 0.543
ATOM 12 C5* 2 S 2 9.661 13.034 13.104 2 0.679
ATOM 13 C4* 2 S 2 8.946 13.436 12.615 2 0.814
ATOM 14 C3* 2 S 2 8.299 13.879 12.107 2 0.950
ATOM 15 P 3 S 3 8.081 14.050 11.915 3 0.000
ATOM 16 O1P 3 S 3 7.084 15.038 10.846 3 0.271
ATOM 17 O2P 3 S 3 6.684 15.562 10.296 3 0.407
ATOM 18 O5* 3 S 3 6.336 16.103 9.738 3 0.543
ATOM 19 C5* 3 S 3 6.027 16.655 9.174 3 0.679
ATOM 20 C4* 3 S 3 5.746 17.216 8.605 3 0.814
ATOM 21 C3* 3 S 3 5.480 17.781 8.035 3 0.950
ATOM 22 P 4 S 4 5.384 17.990 7.824 3 0.000
ATOM 23 COM 1 C 1 6.747 15.474 10.388 3 0.385
ATOM 24 COM 2 C 2 18.152 13.017 15.981 1 0.340
ATOM 25 COM 3 C 3 11.047 12.460 13.896 2 0.441
Similar to the PDB Format:
Column 1 = RECORD NAME
Column 2 = ATOM NUMBER
Column 3 = ATOM TYPE (Points along a spline path have spline points
represented as a DNA backbone while COM points are
represented as type "COM").
Column 4 = RESIDUE NAME (Numbered according to either spline piece
number for splines or COM numbers for COM).
Column 5 = CHAINID (S = Spline and C = COM)
Column 6 = RESIDUE NUMBER (Same as Column 4)
Column 7 = X-COOR | These X, Y, Z-COOR are interpolated points
Column 8 = Y-COOR | for splines and projection points for COM
Column 9 = Z-COOR |
Column 10= Spline Piece (Represents the spline piece that the point
was taken from).
Column 11= TVAL (Represents the T-value from a specific spline piece
identified in Column 10). If this TVAL is substituted
into its corresponding spline piece (from Column 10 which
will look like At^3+Bt^2+Ct+D), this will give the
corresponding X-COOR, Y-COOR, and Z-COOR.
------------------------------------------------------------------------------
Helix Restraint Potential (CONS HELIx)
Questions and comments regarding CONS HELIx should be directed to
----------------------------------------------------------------------------
Wonpil Im (wonpil@ku.edu); Jinhyuk Lee (mack97hyuk@gmail.com);
Taehoon Kim (comboy94@gmail.com); Sunhwan Jo (sunhwanj@gmail.com)
Center for Bioinformatics/Dept. of molecular biosciences, Univ. of Kansas
References:
1. Jinhyuk Lee and Wonpil Im, J. Comput. Chem., 28, 669(2007)
2. Jinhyuk Lee and Wonpil Im, Chem. Phys. Lett., 441, 132(2007)
3. C.Chothia, J.Mol.Biol. 145, 215(1981)
------------------------------------------------------------------------------
[SYNTAX CONS HELIx]
Syntax:
CONS { HELIx } DISTance <real> FORCe <real> -
{ BHG } [SELE 1st-atom-selection END] [SELE 2nd-atom-selection END] -
UDISt <int> STEP <int>
CONS { HELIx } { [CROSs] [HINGe] } ANGLe <real> FORCe <real> -
{ BHG } [SELE 1st-atom-selection END] [SELE 2nd-atom-selection END] -
UANG <int> STEP <int>
CONS { HELIx } { TilX } ANGLe <real> FORCe <real> -
{ BHG } { TilY } [SELE atom-selection END] -
{ TilZ } UANG <int> STEP <int>
CONS { HELIx } ROTH { RotX } ANGLe <real> FORCe <real> REFA <int> -
{ BHG } { RotY } [SELE atom-selection END] -
{ RotZ } UANG <int> STEP <int>
Single selection - Tilt angle constraint or Rotation angle constraint
Double selection - Cross angle constraint or Hinge angle constraint
CROSs : default option - Crossing angle constraint
HINGe : Hinge angle constraint
HELIx : for helix
BHG : for beta-hairpin
CONS HELIx RESEt ! reset CONS HELIx
------------------------------------------------------------------------------
Details of CONS HELIx commands
1) The DISTannce command
The CONS HELIx DISTance command will setup a helix-helix distance
restraint between two selected helices. The detail formalizm and description
are in J. Comput. Chem., 28:669-680(2007).
2) The CROSs/HINGe command
The CONS HELIx CROSs command will setup a helix-helix crossing angle
restraint between two selected helices. The detail formalizm and description
are in J. Comput. Chem., 28:669-680(2007).
The CONS HELIx HINGe command will setup a helix-helix hinge angle
restraint between two selected helices.
3) The ANGLe command
The CONS HELIx ANGLe command will setup a helix tilt angle restraint
of selected helix. The helix tilt (tau) is defined as the angle between helical
principal axis and Z-axis (default). The reference axis can be changed by extra
keywords: (TilX (X-axis),TilY (Y-axis), and TilZ (Z-axis)).
4) The ROTH ANGLe command
The CONS HELIx ROTH ANGLe command will setup a helix rotation angle
restraint of selected helix. The helix rotation (rho) is defined as the angle
between the perpendicular vector (rs) from the helical axis to the selected Ca
atom (keyword: REFA) and the projection vector (zp) of the Z-axis (default) onto
the plane made by the second and third principal axes (see Figure 1, Biophys. J.,
99:175-183 (2010)). The default Z-axis can be changed by extra keywords:
(RotX (X-axis), RotY (Y-axis), and RotZ (Z-axis)).
5) Energy related properties:
'ECHD' - Helix-helix distance restraint energy
'ECHA' - Helix-helix cross/hinge angle restraint energy
'ECHT' - Helix tilt restraint energy
'ECHR' - Helix rotation restraint energy
6) COOR HELIx substitution parameters
Since CONS HELIx incoperate with COOR HELIx command, the following
substitution parameters are specified:
'MIND' - Helix-helix distance
'OMEG' - Helix-helix cross angle
'HANG' - Helix-helix hinge angle
'TANG' - Helix tilt angle
'ROTA' - Helix rotation angle
7) Examples of usage
7-1) To setup a restraint with a force constant of 200.0 kcal/(mol Ang^2) for
a helix-helix distance of 10 angstroms between two helices and to print the
distance to a file linked to a fortran unit 11 every 100 step during simulation:
define helixa sele segid PROA .and. type CA end
define helixb sele segid PROB .and. type CA end
open write card unit 11 name dist.dat
cons helix dist 10.0 force 100.0 select helixa end select helixb end -
udist 11 step 100
7-2) To setup a restraint with a force constant of 70.0 kcal/(mol rad^2) for
a helix-helix crossing angle of 45 degree between two helices and to print the
angle to a file linked to a fortran unit 11 every 100 step during simulation:
define helixa sele segid PROA .and. type CA end
define helixb sele segid PROB .and. type CA end
open write card unit 11 name dist.dat
cons helix cross 45.0 force 35.0 select helixa end select helixb end -
uang 11 step 100
7-3) To setup a restraint with a force constant of 6000.0 kcal/(mol rad^2) for
a helix tilt angle of 45 degree respect to Z-axis (defalut) and to print the
angle to a file linked to a fortran unit 11 every 100 step during simulation:
define helixa sele segid PROA .and. type CA end
open write card unit 11 name angle.dat
cons helix angle 45.0 force 3000.0 select helixa end -
uang 11 step 100
7-4) To setup a restraint with a force constant of 200.0 kcal/(mol rad^2) for
a helix rotation angle of 30 degree using Ca atom in 10th residue as an internal
reference (Biophys. J., 99:175-183 (2010)) and to print the angle to a file
plinked to a fortran unit 11 every 100 step during simulation:
define helixa sele segid PROA .and. type CA end
open write card unit 11 name rotation.dat
cons helix roth angle 30.0 force 100.0 refa 10 select helixa end -
uang 11 step 100
NOTE: The helix restraint does not have one-half in the harmonic form, so
the force constants must be a half of real value if a one-half harmonic form
is considered for any post-analysis.