mmfp (c46b1)
Syntax of basic MMFP commands
GEO reset
GEO [MAXGEO integer] [shape_specification] [position_spec] [RCM]
[potential_spec] [atom_selection] [ DISTANCE atom_selection]
[ ADISTANCE atom_selection atom_selection ] [PERP]
[ ANGLE atom_selection atom_selection ]
[ DIHEDRAL 3 X atom_selection ]
[ IUMMFP unit]
SSBP reset
SSBP [atom_selection] [atom_selection] [ssbp_specification]
BHEL [atom_selection]
SHEL [atom_selection] [shell_options-specification]
VMOD RESEt
VMOD INIT MXMD integer UMDN integer [NATM integer] -
KROT real KCGR real UOUT integer NSVQ integer [atom selection]
{ VMOD ADD IMDN integer KMDN real QN real }
{ VMOD CHANge NREStraint integer KMDN real QN real }
EPR NSPINLABELS integer NREPLICA integer KENPP real SIG2EPR real -
[atom_selection] -
DELPPP real NPTOT integer NPPP integer UNIT 50
BPCMap NBTP integer LAMBDA real DIM integer UNIT integer -
DIHE 8x[atom selection]
shape_specification:== { [SPHERE] } [XREF real] [YREF real] [ZREF real] -
[TREF real]
{ CYLINDER } [XDIR real] [YDIR real] [ZDIR real]
{ PLANAR }
potential_spec:== { HARMonic } { INSIDE } [FORCE real] -
[DROFF real] [DTOFF real]
{ QUARtic } { OUTSIDE } [P1 real] [P2 real]
{ EXPOnent } { SYMMETRIC }
{ GAUSsian } { RMAX FORCE 3x[atom selection]}
{ SAWOod }
ssbp_pecification:== KIRKWOOD NMULT [integer (15)] [DIEC real] [RADI real]
[DRDIE real] CAVITY HSR ANGU [EMP1 real] [EMP2 real]
shell_options-specification:==
DRSH [real (8.0)] RELA [real (0.00001)] SCO [real (0.0)]
PFINAL [real (1.0)] CUT [real (2.0)] RWEL [real (0.25)]
FOCO1 [real (3.0)] FOCO2 [real (15.0)] CHCO [real (0.00001)]
SPACE [integer (1000000)] UPDF [integer (10)] CHFR [integer (1000)]
atom-selection:== (see » select )
GEO reset
GEO [MAXGEO integer] [shape_specification] [position_spec] [RCM]
[potential_spec] [atom_selection] [ DISTANCE atom_selection]
[ ADISTANCE atom_selection atom_selection ] [PERP]
[ ANGLE atom_selection atom_selection ]
[ DIHEDRAL 3 X atom_selection ]
[ IUMMFP unit]
SSBP reset
SSBP [atom_selection] [atom_selection] [ssbp_specification]
BHEL [atom_selection]
SHEL [atom_selection] [shell_options-specification]
VMOD RESEt
VMOD INIT MXMD integer UMDN integer [NATM integer] -
KROT real KCGR real UOUT integer NSVQ integer [atom selection]
{ VMOD ADD IMDN integer KMDN real QN real }
{ VMOD CHANge NREStraint integer KMDN real QN real }
EPR NSPINLABELS integer NREPLICA integer KENPP real SIG2EPR real -
[atom_selection] -
DELPPP real NPTOT integer NPPP integer UNIT 50
BPCMap NBTP integer LAMBDA real DIM integer UNIT integer -
DIHE 8x[atom selection]
shape_specification:== { [SPHERE] } [XREF real] [YREF real] [ZREF real] -
[TREF real]
{ CYLINDER } [XDIR real] [YDIR real] [ZDIR real]
{ PLANAR }
potential_spec:== { HARMonic } { INSIDE } [FORCE real] -
[DROFF real] [DTOFF real]
{ QUARtic } { OUTSIDE } [P1 real] [P2 real]
{ EXPOnent } { SYMMETRIC }
{ GAUSsian } { RMAX FORCE 3x[atom selection]}
{ SAWOod }
ssbp_pecification:== KIRKWOOD NMULT [integer (15)] [DIEC real] [RADI real]
[DRDIE real] CAVITY HSR ANGU [EMP1 real] [EMP2 real]
shell_options-specification:==
DRSH [real (8.0)] RELA [real (0.00001)] SCO [real (0.0)]
PFINAL [real (1.0)] CUT [real (2.0)] RWEL [real (0.25)]
FOCO1 [real (3.0)] FOCO2 [real (15.0)] CHCO [real (0.00001)]
SPACE [integer (1000000)] UPDF [integer (10)] CHFR [integer (1000)]
atom-selection:== (see » select )
Top
Details of basic MMFP commands
1) GEO RESET
Cancels all restraints in GEO free all space allocated on the HEAP
2) GEO [MAXGEO int]
Allocate space on the HEAP to be used for all subsequent GEO potential terms.
By default, MAXGEO is set to NATOM unless specified. The MMFP subroutine calls
WRNDIE if there is not enough space allocated.
The keyword IUMMFP followed by a unit number will cause the position R,
or the angle (degrees) for that constraint to be written to that file.
By default no writing is performed for each GEO restraint.
3) RCM key word
With the keyword RCM any restraints is not applied to each individual
atoms of a selection but applied to the center of mass of the selected atoms.
5) [shape_specification]
The shape of the potential is chosen from SPHERE, CYLINDER or PLANE key words,
SPHERE is the default. The shape specification gives the origin
(XREF, YREF, ZREF, or TREF for angles) and the orientation (XDIR, YDIR, ZDIR)
of a vector such that a sphere, plane or cylinder may be defined. Using the
shape_specification the potential is calculated from the
general distance from a (x,y,z) reference point (SPHERE), distance from
an axis (CYLINDER) or distance from a plane (PLANE). By default, all
values are zero and the origin of the boundary is at (0.0,0.0,0.0).
If the shape of the boundary requires a unit vector (true for cylinder
and plane), and no values are given the subroutine will call WRNDIE.
6) [potential_spec] [HARMonic]
[QUARtic]
[EXPOnential]
[GAUSsian]
[SAWOod]
The potential specification has a number of
parameters: [FORCE real] is the amplitude of the potential term
[P1 real] is a parameter used in the quartic, the gaussian,
the exponetntial and the Saxon-Wood-type potential
[P2 real] parameter used in the Saxon-Wood-type potential
[DROFF real] is an offset distance such that GEO(r) = 0 if r<droff
[DTOFF real] is an offset angle such that GEO(theta) = 0
if theta<dtoff
[INSIDE] the potential used only for r-droff<0
[OUTSIDE] the potential used is only for r-droff>0
[SYMMETRIC] the potential used is for |r-droff|
They determine which kind of potential function will be used in combination
with the geometrical shape. The default is a harmonic potential. A fourth
order polynomial can be used with the key word QUARTIC, the potential has
the form: GEO(r) = FORC*DELTA**2*(DELTA**2-P1), with DELTA=(R-DROFF).
Using the parameters [FORCE 0.2 P1 2.25] the QUARTIC potential can be used
to setup a spherical boundary potential with a well depth of -0.25 kcal/mol
at r=DROFF+1 followed by a smoothly rising repulsion. Such potential is
appropriate for a water sphere of radius DROFF+1.5 and is very similar
to that used in SBOUND, see » sbound
The key word EXPO defines a exponential potential to mimic interfacial
solvation effects:
= HALF*FORC*EXP(-DELTA/P1), for r > DROFF
= FORC*(1 - HALF*EXP(+DELTA/P1), for r < DROFF
When defined in combination with PLANE shape_specification, this potential
reproduces the "hydrophobic" potential used for transmembrane polypeptide
by O. Edholm. and F. Jahnig, Biophys. Chem. 30, 279-292 (1988).
The key word GAUSS defines a similar gaussian potential to mimic interfacial
solvation effects. The parameter P1 gives the width of the interface.
The keyword SAWO defines an exponential Saxon-Wood-type flat-bottom
potential of the form:
= FORC/( 1 + Exp((P2-DELTA)/P1) ) - V(0) for r > DROFF
= FORC/( 1 + Exp((P2+DELTA)/P1) ) - V(0) for r < DROFF
where P1 is responsible for the steepness of the potential and P2
determines the width (the distance between the two inflection points)
of the restraint. V(0) is an offset correction to ensure a value of
zero at the equilibrium point.
This restraint should be helpful e.g., for binding free energy
difference calculations (it doesn't perturb the potential energy
landscape of the system within an adjustable range).
The RMAX option works with the HARM potential to allow FIRES (
flexible inner region ensemble separator, Rowley, C. N.; Roux, B.
J. Chem. Theory Comput. 2012, 8, 3526-3535). The current implementation
requires three selections. The first selection defines the origin of the
FIRES potential; the second selection defines the inner region, while the
third selection defines the outer region. See an example below.
7) DISTANCE key word With the keyword DISTANCE a restraint is setup
between two sets of atoms or between their center of mass if the key
word RCM is used. A second atom selection must be specified.
8) ADISTANCE key word With the keyword ADIS a restraint is setup
between one atom set, and two other sets of atoms, such that the position
of the first selection is constrained at some distance parallel to
the axis joining the centres of mass of the second and third atom selections.
A second and third atom selection must be specified. The keyword PERP
will instead constrain the first atom selection at a distance
perpendicular to the axis vector.
9) ANGLE keyword With the keyword ANGLE a restraint is setup between 3
sets of atoms or their center of masses if the keyword RCM is
used. Three sets of atom selections must be made, note that the force
constant is per radian**2 and NOT per degree**2 even though the TREF
(theta-reference, equivalent to DROFF of v29)
variable (angle constraint) is to be specified in degrees.
Specification of DTOFF variable can allow shifting of the potential
away from TREF, as is useful in the INSIde restraint.
10) DIHEDRAL keyword With the keyword DIHEDRAL a restraint is setup
between 4 sets of atoms or their center of masses if the keyword RCM
is used. Four sets of atom selections must be made, note that the
force constant is per radian**2 and NOT per degree**2 even though the
TREF (equivalent to DROFF) variable (dihedral constraint) is to be
specified in degrees.
An offset of DTOFF may also be used for this restraint.
11) SSBP key word
Stands for Spherical Solvent Boundary Potential. Current implementation of
the method described in Beglov & Roux, J. Chem. Phys., 100:9050 (1994).
The method follows from a rigorous reduction of the multi-dimensional
configuration integral from N solvent molecules (10**23) to "n" solvent
molecules (e.g., 1 to 1000).
The SSBP potential corresponds to a constant temperature and constant
pressure system. The non-bonded interactions must be treated with EXTENDED
electrostatics otherwise the system is unstable. There are several
contributions to the boundary potential of mean force: HSR (hard sphere
restriction) is a term setting the external pressure and surface tension;
CAVITY ressembles to the standard stochastic boundary potential and
corresponds to the van der Waals interactions; KIRKWOOD is the multipolar
expansion for the reaction field due to a dielectric continuum surrounding a
cavity containing a charge distribution; ANGU is an angular correction that
works for three sites water models and is used to restore the isotropic
angular distribution near the edge of the sphere. EMP1 and EMP2
are two parameters for empirical gaussian potential (Deng, Y and Roux B.
J. Phys. Chem. B, 108 (42), 16567--16576).
The magnitude of the gaussian is controlled by EMP1,
which has a default value of 1.1 kcal/mol.
The width of the gaussian potential is controlled by EMP2, which
has a default value of 0.008 angstrom^-2. The empirical correction
reduces the pressure in the simulation sphere, which is essential
for correct free energy simulations. The variable radius of
the sphere is calculated on the fly and does not need to be specified.
The first atom selection flags the atoms for which the VDW and the ANGU
potentials are applied. It also determines the radius of the boundary sphere.
The second selection is optional. If present it flags those atoms that
determine the radius of the boundary sphere. By default, only the first
flags everything; the second selection is there if one wants to remove
some part of the system to determine the radius of the boundary sphere
(such as a large part of a protein in an active site simulation).
For bulk water sphere simulations, the first atom selection for should
be "select type OH2 end". The second atoms selection is optional and
could be "select type OH2 end" or could be "select (.not. type H*) end".
In NO CASE should the second selection includes the water hydrogens, since
the results were NOT parametrized for this selection.
12) BHEL key word
This key word is used to set up simulations using the primary hydration
shell (PHS) model as described in Beglov & Roux, Biopolymers 35: 171-178
(1995).
The method was later modified to allow constant pressure simulations,
and to improve it's efficiency (for details see: M B Hamaneh, and M Buck,
Refinement of the primary hydration shell model for molecular dynamics
simulations of large proteins, Journal of Computational Chemistry, in press).
In this method the protein of interest is solvated using only a thin shell
of water, and, to prevent evaporation of the solvent, a half-harmonic force
is applied to the water molecules whose distance from the nearest protein
atom is larger than a certain value. To reduce the pressure on the system,
a small outward half-harmonic force is also applied to the water molecules
that are close to the solvent-vacuum boundary. By adjusting the ratio of the
outward and inward forces the pressure of the system is held constant at the
desired value. As described above, in the PHS method at each step the nearest
protein atom to each water molecule has to be found. To do this two atom
selections (one selection for protein atoms and the other for water molecules)
are required. The selection command for the protein atoms comes after the key
word BHEL. The selection usually contains all heay (not hydrogens) protein
atoms, but in large systems one can exclude the atoms that are deep inside
the protein. For water selection the key word SHEL is used (described below).
It is worth mentioning that the PHS code works in parallel.
13) SHEL key word
This key word is used after BHEL to complete the set-up of the
primary hydration shell (PHS) method (described above). The atom selection
should select ALL water oxygen atoms. There are several parameters in the
PHS model that can be set by the user. These parameters should be defined after
the atom selection. Here is a brief description of these parameters:
DRSH The thickness of the water shell. The initial value of DRSH
is set by the user. The program then adjusts this parameter to keep
the water density close to the right value. During a simulation the
value of DRSH can be accessed (using ?DRSH), but it is not saved in
restart files, and so the user must re-define this paramter when
the simulation is restarted. In other words, DRSH must be printed
out at the very end of each simulation, so it could be used as a
starting value if the simulation is going to be restatrted.
At the beginning of a simulation The thickness of the shell (DRSH)
should be usually set to a value that is about two Angstroms
(approximately the Van der Waals radus of a protein heavy atom)
larger than the distance between the farthest water oxygen from
the protein. For example, if you keep only water molecules that are
within 10 A from any protein atom, DRSh should be initially set
to 8 A.
CHFR The step frequncy at which DRSH is adjusted to have the right
water density.
RELA A relaxation parameter that determines how much DRSH is changed
every CHFR steps. In the initial minimization stage this parameter
should be set to zero.
PFINAL The desired pressure.
FOCO1 The force constant of the external force (that prevents evaporation)
for water molecules whose nearest protein residue is non-polar.
Different force constants may be used depending on the polarity of
the nearest protein residue.
FOCO2 The force constant if the nearest protein residue is polar. In Most
simulations FOCO2 may safely chosen to be equal to FOCO1. If the
simulation results in desolvation of the hydrophbic residues, using
a FOCO1 that is larger than FOCO2 usually helps to have a more
uniform water distribution. However, the difference between the two
force constants should not be large.
RWEL RWEL*DRSH is the thickness of the region in which the outward force
is applied to the water molecules. This force acts on any water
molecule whose distance from the nearest protein atom, d, is between
DRSH+a-DRSH*RWEL and DRSH+a where a is the Van der waals radius of
the protein atom.
SCO The ratio of the outward and inward external forces. Adjusting this
parameter at each simulation step controls the pressure. During
a simulation the value of SCO can be accessed (using ?SCO), but it
is not saved in restart files, and so the user must re-define this
paramter when the simulation is restarted. In other words, SCO must
be printed out at the very end of each simulation, so it could be
used as a starting value if the simulation is going to be restatrted.
CHCO The coefficient that determines how much OSC is changed at each step.
In the initial minimization stage this parameter should be set to
zero.
SPACE Determines the size of the grid for volume calculations.
See description of the VOLUME command in corman.info.
CUT The cut-off for determinning whether or not a protein atom is
a "neighbor" of a particular water molecule. To efficiently find
the nearest protein atom to each water molecule, only the water
molecules that are within the region defined by RWEl (described
above) are considered for distance calculation. Also for each water
in that region a list of neighboring protein atoms is constructed.
Any protein heavy atom whose distance from the water molecule is
less than DRSH*CUT is a member of the neighbor list. CUT must be
bigger than one and should be chosen in such a way that CUT*DRSH is
at least 5 Angstrom larger than DRSH.
UPDF The step frequency for updating the water and protein lists.
For a typical system, the default value (10) should work fine.
14) VMOD key word
The VMOD facility (David Perahia, Sylvain Frederic & Charles H. Robert
2002-2008) is used to add one or more terms to the potential energy, each
corresponding to a restraint to a given mrms projection on a normal
mode or other 3N-dimensional vector. An appropriate reference is Floquet
et al. (2006) FEBS Lett. 580, 5130-6. This facility is compatible with
parallel operation.
The command has several forms: initialization, adding a specification
of a mode restraint, changing the restraint parameters, printing data
concerning the current structrue, and resetting (to free the heap).
VMOD INIT performs the initialization of the VMOD facility:
MXMD maximum number of mode restraints to add
KROT harmonic force constant for rotational restraint of the system
KCGR harmonic force constant for translational restraint of the system
UMDN the unit number of the open modes file. The keyword CARD can be used
to specify a card-formatted modefile, the default is a binary file
NATM number of atoms in the modefile (defaults to number in current PSF)
UOUT unit number (formatted output) to write normal mode mrms coordinates
and restraint energies at a given step
NSVQ frequency in terms of minimization or dynamics steps for writing
detailed data to UOUT
An optional atom selection permits restricting the restraint force to the
desired subset of atoms present in the mode file.
Note: The reference structure (e.g., structure for which the modes were
calculated) must be in the main coords when invoking this command!
VMOD ADD restraint statement(s) must (each) specify the following
IMDN is the mode number in the mode file
KMDN is the harmonic force constant (kcal/mol-A) for the mrms restraint
QN is the desired target mrms value
VMOD CHANge restraint statement(s) must (each) specify the following
NREStraint is the constraint (not mode) number (i.e., 1...MXMD)
KMDN is the new harmonic force constant (defaults to current value)
QN is the new desired target mrms value (defaults to current value)
VMOD PRINt summarizes the mode projections and energies for the current structure
VMOD RESET removes all existing VMOD restraints. It will give an error
unless a VMOD INIT command has already been executed.
In minimization or dynamics runs, the total restraint energy (Emode+Etrans+Erotat)
is reported in the "MINI MMFP2>" or "DYNA MMFP2>" output, while more detailed
data is written to the UOUT file at the desired frequency as specified in the
VMOD INIT statement.
14) EPR key word
This key word is used to set up the Restrained-Ensemble (RE) Molecular Dynamics
simulation (Roux B. and Islam, S. M. J. Phys. Chem. B, 2013, 117, 4733-39) which
is shown to be able to systematically correct and refine a series of distorted T4
lysozyme structures (Islam, S. M. and Roux B. J. Phys. Chem. B, 2013, 117, 4740-56).
In this simulation, it is required to create a system with multiple copies of
spin-labels, which yield a total of N2 distances for each pair of spin-labels at
every step in a molecular dynamics simulation. The ensemble-averaged instantaneous
histogram produced by the multiple replica are then matched with the target experimental
EPR/DEER histogram via an energy restraint using a large harmonic force constant. Here
is a brief description of various parameters in EPR:
NSPINLABELS Number of spin-labels at various positions in the system.
NREPLICA Number of copies/replicas for each spin-labels in a specific site of the system
KENPP A large harmonic force constant used to impose the energy restraint
SIG2EPR Natural spread ? of the Gaussian for each histogram. One may keep this fixed at 1.7
DELPPP Bin spacing in the EPR/DEER distance distribution. The bin spacing must be equal for all bins.
NPTOT Number of spin-pair distributions from EPR/DEER spectroscopy.
NPPP Total number of bins in the EPR/DEER histogram.
UNIT The number that is used to call the file with the EPR/DEER distributions.
15) BPCMap key word
BPCMap introduces biasing potentials using a 2D grid-based CMAP to any
set of two (usually consequtive) dihedral angles for use in Hamiltonian
replica exchange simulations (Yang M, MacKerell Jr A D. J. Chem. Theory Comput.,
2015, 11(2): 788-799.). It can be applied, for example, to the peptide backbone
phi/psi dihedrals or to glycosidic linkage dihedrals in carbohydrates (Yang M,
Huang J, and MacKerell Jr A D., J. Chem. Theory Comput., 2015, 11(6): 2855-2867.).
Following the keyword BPCMAP, the integer NBTP integer indicates the
number of indvidual bpCMAPs that will be read. Each bpCMAP is then
specified individually as indicated by the LAMBDA value, the dimension
DIM of the map, the UNIT from which the specific bpCMAP is read and
the DIHEdrals to which the bpCMAP is being applied. Typically the
same value of lambda is used for each bpCMAP for a given replica
(though the current implementation allows this to be varied) and the
same bpCMAP can be read multiple times from the same UNIT. See the
example input below. Note that the bpCMAP energy is included with the
CMAPs energy reported in CHARMM. To access the bpCMAP energy
contribution an energy calculation without invoking bpCMAP must be
perfomed and the difference in the CMAPs energy term obtained.
NBTP [integer]: Number of bpCMAPs.
LAMBDA [real]: scaling factor of the biased potential CMAP: the default value is 1.d0 .
DIM [integer]: The dimensions of the specific bpCMAP: the default value is 24.
UNIT [integer]: The previously opened bpCMAP UNIT number.
DIHE: Specify the two dihedrals to which the bpCMAP is being
applied. 8x[atom_selection]. Note that each atom selection should only
select one atom.
END: to finish reading bpCMAPs
Details of basic MMFP commands
1) GEO RESET
Cancels all restraints in GEO free all space allocated on the HEAP
2) GEO [MAXGEO int]
Allocate space on the HEAP to be used for all subsequent GEO potential terms.
By default, MAXGEO is set to NATOM unless specified. The MMFP subroutine calls
WRNDIE if there is not enough space allocated.
The keyword IUMMFP followed by a unit number will cause the position R,
or the angle (degrees) for that constraint to be written to that file.
By default no writing is performed for each GEO restraint.
3) RCM key word
With the keyword RCM any restraints is not applied to each individual
atoms of a selection but applied to the center of mass of the selected atoms.
5) [shape_specification]
The shape of the potential is chosen from SPHERE, CYLINDER or PLANE key words,
SPHERE is the default. The shape specification gives the origin
(XREF, YREF, ZREF, or TREF for angles) and the orientation (XDIR, YDIR, ZDIR)
of a vector such that a sphere, plane or cylinder may be defined. Using the
shape_specification the potential is calculated from the
general distance from a (x,y,z) reference point (SPHERE), distance from
an axis (CYLINDER) or distance from a plane (PLANE). By default, all
values are zero and the origin of the boundary is at (0.0,0.0,0.0).
If the shape of the boundary requires a unit vector (true for cylinder
and plane), and no values are given the subroutine will call WRNDIE.
6) [potential_spec] [HARMonic]
[QUARtic]
[EXPOnential]
[GAUSsian]
[SAWOod]
The potential specification has a number of
parameters: [FORCE real] is the amplitude of the potential term
[P1 real] is a parameter used in the quartic, the gaussian,
the exponetntial and the Saxon-Wood-type potential
[P2 real] parameter used in the Saxon-Wood-type potential
[DROFF real] is an offset distance such that GEO(r) = 0 if r<droff
[DTOFF real] is an offset angle such that GEO(theta) = 0
if theta<dtoff
[INSIDE] the potential used only for r-droff<0
[OUTSIDE] the potential used is only for r-droff>0
[SYMMETRIC] the potential used is for |r-droff|
They determine which kind of potential function will be used in combination
with the geometrical shape. The default is a harmonic potential. A fourth
order polynomial can be used with the key word QUARTIC, the potential has
the form: GEO(r) = FORC*DELTA**2*(DELTA**2-P1), with DELTA=(R-DROFF).
Using the parameters [FORCE 0.2 P1 2.25] the QUARTIC potential can be used
to setup a spherical boundary potential with a well depth of -0.25 kcal/mol
at r=DROFF+1 followed by a smoothly rising repulsion. Such potential is
appropriate for a water sphere of radius DROFF+1.5 and is very similar
to that used in SBOUND, see » sbound
The key word EXPO defines a exponential potential to mimic interfacial
solvation effects:
= HALF*FORC*EXP(-DELTA/P1), for r > DROFF
= FORC*(1 - HALF*EXP(+DELTA/P1), for r < DROFF
When defined in combination with PLANE shape_specification, this potential
reproduces the "hydrophobic" potential used for transmembrane polypeptide
by O. Edholm. and F. Jahnig, Biophys. Chem. 30, 279-292 (1988).
The key word GAUSS defines a similar gaussian potential to mimic interfacial
solvation effects. The parameter P1 gives the width of the interface.
The keyword SAWO defines an exponential Saxon-Wood-type flat-bottom
potential of the form:
= FORC/( 1 + Exp((P2-DELTA)/P1) ) - V(0) for r > DROFF
= FORC/( 1 + Exp((P2+DELTA)/P1) ) - V(0) for r < DROFF
where P1 is responsible for the steepness of the potential and P2
determines the width (the distance between the two inflection points)
of the restraint. V(0) is an offset correction to ensure a value of
zero at the equilibrium point.
This restraint should be helpful e.g., for binding free energy
difference calculations (it doesn't perturb the potential energy
landscape of the system within an adjustable range).
The RMAX option works with the HARM potential to allow FIRES (
flexible inner region ensemble separator, Rowley, C. N.; Roux, B.
J. Chem. Theory Comput. 2012, 8, 3526-3535). The current implementation
requires three selections. The first selection defines the origin of the
FIRES potential; the second selection defines the inner region, while the
third selection defines the outer region. See an example below.
7) DISTANCE key word With the keyword DISTANCE a restraint is setup
between two sets of atoms or between their center of mass if the key
word RCM is used. A second atom selection must be specified.
8) ADISTANCE key word With the keyword ADIS a restraint is setup
between one atom set, and two other sets of atoms, such that the position
of the first selection is constrained at some distance parallel to
the axis joining the centres of mass of the second and third atom selections.
A second and third atom selection must be specified. The keyword PERP
will instead constrain the first atom selection at a distance
perpendicular to the axis vector.
9) ANGLE keyword With the keyword ANGLE a restraint is setup between 3
sets of atoms or their center of masses if the keyword RCM is
used. Three sets of atom selections must be made, note that the force
constant is per radian**2 and NOT per degree**2 even though the TREF
(theta-reference, equivalent to DROFF of v29)
variable (angle constraint) is to be specified in degrees.
Specification of DTOFF variable can allow shifting of the potential
away from TREF, as is useful in the INSIde restraint.
10) DIHEDRAL keyword With the keyword DIHEDRAL a restraint is setup
between 4 sets of atoms or their center of masses if the keyword RCM
is used. Four sets of atom selections must be made, note that the
force constant is per radian**2 and NOT per degree**2 even though the
TREF (equivalent to DROFF) variable (dihedral constraint) is to be
specified in degrees.
An offset of DTOFF may also be used for this restraint.
11) SSBP key word
Stands for Spherical Solvent Boundary Potential. Current implementation of
the method described in Beglov & Roux, J. Chem. Phys., 100:9050 (1994).
The method follows from a rigorous reduction of the multi-dimensional
configuration integral from N solvent molecules (10**23) to "n" solvent
molecules (e.g., 1 to 1000).
The SSBP potential corresponds to a constant temperature and constant
pressure system. The non-bonded interactions must be treated with EXTENDED
electrostatics otherwise the system is unstable. There are several
contributions to the boundary potential of mean force: HSR (hard sphere
restriction) is a term setting the external pressure and surface tension;
CAVITY ressembles to the standard stochastic boundary potential and
corresponds to the van der Waals interactions; KIRKWOOD is the multipolar
expansion for the reaction field due to a dielectric continuum surrounding a
cavity containing a charge distribution; ANGU is an angular correction that
works for three sites water models and is used to restore the isotropic
angular distribution near the edge of the sphere. EMP1 and EMP2
are two parameters for empirical gaussian potential (Deng, Y and Roux B.
J. Phys. Chem. B, 108 (42), 16567--16576).
The magnitude of the gaussian is controlled by EMP1,
which has a default value of 1.1 kcal/mol.
The width of the gaussian potential is controlled by EMP2, which
has a default value of 0.008 angstrom^-2. The empirical correction
reduces the pressure in the simulation sphere, which is essential
for correct free energy simulations. The variable radius of
the sphere is calculated on the fly and does not need to be specified.
The first atom selection flags the atoms for which the VDW and the ANGU
potentials are applied. It also determines the radius of the boundary sphere.
The second selection is optional. If present it flags those atoms that
determine the radius of the boundary sphere. By default, only the first
flags everything; the second selection is there if one wants to remove
some part of the system to determine the radius of the boundary sphere
(such as a large part of a protein in an active site simulation).
For bulk water sphere simulations, the first atom selection for should
be "select type OH2 end". The second atoms selection is optional and
could be "select type OH2 end" or could be "select (.not. type H*) end".
In NO CASE should the second selection includes the water hydrogens, since
the results were NOT parametrized for this selection.
12) BHEL key word
This key word is used to set up simulations using the primary hydration
shell (PHS) model as described in Beglov & Roux, Biopolymers 35: 171-178
(1995).
The method was later modified to allow constant pressure simulations,
and to improve it's efficiency (for details see: M B Hamaneh, and M Buck,
Refinement of the primary hydration shell model for molecular dynamics
simulations of large proteins, Journal of Computational Chemistry, in press).
In this method the protein of interest is solvated using only a thin shell
of water, and, to prevent evaporation of the solvent, a half-harmonic force
is applied to the water molecules whose distance from the nearest protein
atom is larger than a certain value. To reduce the pressure on the system,
a small outward half-harmonic force is also applied to the water molecules
that are close to the solvent-vacuum boundary. By adjusting the ratio of the
outward and inward forces the pressure of the system is held constant at the
desired value. As described above, in the PHS method at each step the nearest
protein atom to each water molecule has to be found. To do this two atom
selections (one selection for protein atoms and the other for water molecules)
are required. The selection command for the protein atoms comes after the key
word BHEL. The selection usually contains all heay (not hydrogens) protein
atoms, but in large systems one can exclude the atoms that are deep inside
the protein. For water selection the key word SHEL is used (described below).
It is worth mentioning that the PHS code works in parallel.
13) SHEL key word
This key word is used after BHEL to complete the set-up of the
primary hydration shell (PHS) method (described above). The atom selection
should select ALL water oxygen atoms. There are several parameters in the
PHS model that can be set by the user. These parameters should be defined after
the atom selection. Here is a brief description of these parameters:
DRSH The thickness of the water shell. The initial value of DRSH
is set by the user. The program then adjusts this parameter to keep
the water density close to the right value. During a simulation the
value of DRSH can be accessed (using ?DRSH), but it is not saved in
restart files, and so the user must re-define this paramter when
the simulation is restarted. In other words, DRSH must be printed
out at the very end of each simulation, so it could be used as a
starting value if the simulation is going to be restatrted.
At the beginning of a simulation The thickness of the shell (DRSH)
should be usually set to a value that is about two Angstroms
(approximately the Van der Waals radus of a protein heavy atom)
larger than the distance between the farthest water oxygen from
the protein. For example, if you keep only water molecules that are
within 10 A from any protein atom, DRSh should be initially set
to 8 A.
CHFR The step frequncy at which DRSH is adjusted to have the right
water density.
RELA A relaxation parameter that determines how much DRSH is changed
every CHFR steps. In the initial minimization stage this parameter
should be set to zero.
PFINAL The desired pressure.
FOCO1 The force constant of the external force (that prevents evaporation)
for water molecules whose nearest protein residue is non-polar.
Different force constants may be used depending on the polarity of
the nearest protein residue.
FOCO2 The force constant if the nearest protein residue is polar. In Most
simulations FOCO2 may safely chosen to be equal to FOCO1. If the
simulation results in desolvation of the hydrophbic residues, using
a FOCO1 that is larger than FOCO2 usually helps to have a more
uniform water distribution. However, the difference between the two
force constants should not be large.
RWEL RWEL*DRSH is the thickness of the region in which the outward force
is applied to the water molecules. This force acts on any water
molecule whose distance from the nearest protein atom, d, is between
DRSH+a-DRSH*RWEL and DRSH+a where a is the Van der waals radius of
the protein atom.
SCO The ratio of the outward and inward external forces. Adjusting this
parameter at each simulation step controls the pressure. During
a simulation the value of SCO can be accessed (using ?SCO), but it
is not saved in restart files, and so the user must re-define this
paramter when the simulation is restarted. In other words, SCO must
be printed out at the very end of each simulation, so it could be
used as a starting value if the simulation is going to be restatrted.
CHCO The coefficient that determines how much OSC is changed at each step.
In the initial minimization stage this parameter should be set to
zero.
SPACE Determines the size of the grid for volume calculations.
See description of the VOLUME command in corman.info.
CUT The cut-off for determinning whether or not a protein atom is
a "neighbor" of a particular water molecule. To efficiently find
the nearest protein atom to each water molecule, only the water
molecules that are within the region defined by RWEl (described
above) are considered for distance calculation. Also for each water
in that region a list of neighboring protein atoms is constructed.
Any protein heavy atom whose distance from the water molecule is
less than DRSH*CUT is a member of the neighbor list. CUT must be
bigger than one and should be chosen in such a way that CUT*DRSH is
at least 5 Angstrom larger than DRSH.
UPDF The step frequency for updating the water and protein lists.
For a typical system, the default value (10) should work fine.
14) VMOD key word
The VMOD facility (David Perahia, Sylvain Frederic & Charles H. Robert
2002-2008) is used to add one or more terms to the potential energy, each
corresponding to a restraint to a given mrms projection on a normal
mode or other 3N-dimensional vector. An appropriate reference is Floquet
et al. (2006) FEBS Lett. 580, 5130-6. This facility is compatible with
parallel operation.
The command has several forms: initialization, adding a specification
of a mode restraint, changing the restraint parameters, printing data
concerning the current structrue, and resetting (to free the heap).
VMOD INIT performs the initialization of the VMOD facility:
MXMD maximum number of mode restraints to add
KROT harmonic force constant for rotational restraint of the system
KCGR harmonic force constant for translational restraint of the system
UMDN the unit number of the open modes file. The keyword CARD can be used
to specify a card-formatted modefile, the default is a binary file
NATM number of atoms in the modefile (defaults to number in current PSF)
UOUT unit number (formatted output) to write normal mode mrms coordinates
and restraint energies at a given step
NSVQ frequency in terms of minimization or dynamics steps for writing
detailed data to UOUT
An optional atom selection permits restricting the restraint force to the
desired subset of atoms present in the mode file.
Note: The reference structure (e.g., structure for which the modes were
calculated) must be in the main coords when invoking this command!
VMOD ADD restraint statement(s) must (each) specify the following
IMDN is the mode number in the mode file
KMDN is the harmonic force constant (kcal/mol-A) for the mrms restraint
QN is the desired target mrms value
VMOD CHANge restraint statement(s) must (each) specify the following
NREStraint is the constraint (not mode) number (i.e., 1...MXMD)
KMDN is the new harmonic force constant (defaults to current value)
QN is the new desired target mrms value (defaults to current value)
VMOD PRINt summarizes the mode projections and energies for the current structure
VMOD RESET removes all existing VMOD restraints. It will give an error
unless a VMOD INIT command has already been executed.
In minimization or dynamics runs, the total restraint energy (Emode+Etrans+Erotat)
is reported in the "MINI MMFP2>" or "DYNA MMFP2>" output, while more detailed
data is written to the UOUT file at the desired frequency as specified in the
VMOD INIT statement.
14) EPR key word
This key word is used to set up the Restrained-Ensemble (RE) Molecular Dynamics
simulation (Roux B. and Islam, S. M. J. Phys. Chem. B, 2013, 117, 4733-39) which
is shown to be able to systematically correct and refine a series of distorted T4
lysozyme structures (Islam, S. M. and Roux B. J. Phys. Chem. B, 2013, 117, 4740-56).
In this simulation, it is required to create a system with multiple copies of
spin-labels, which yield a total of N2 distances for each pair of spin-labels at
every step in a molecular dynamics simulation. The ensemble-averaged instantaneous
histogram produced by the multiple replica are then matched with the target experimental
EPR/DEER histogram via an energy restraint using a large harmonic force constant. Here
is a brief description of various parameters in EPR:
NSPINLABELS Number of spin-labels at various positions in the system.
NREPLICA Number of copies/replicas for each spin-labels in a specific site of the system
KENPP A large harmonic force constant used to impose the energy restraint
SIG2EPR Natural spread ? of the Gaussian for each histogram. One may keep this fixed at 1.7
DELPPP Bin spacing in the EPR/DEER distance distribution. The bin spacing must be equal for all bins.
NPTOT Number of spin-pair distributions from EPR/DEER spectroscopy.
NPPP Total number of bins in the EPR/DEER histogram.
UNIT The number that is used to call the file with the EPR/DEER distributions.
15) BPCMap key word
BPCMap introduces biasing potentials using a 2D grid-based CMAP to any
set of two (usually consequtive) dihedral angles for use in Hamiltonian
replica exchange simulations (Yang M, MacKerell Jr A D. J. Chem. Theory Comput.,
2015, 11(2): 788-799.). It can be applied, for example, to the peptide backbone
phi/psi dihedrals or to glycosidic linkage dihedrals in carbohydrates (Yang M,
Huang J, and MacKerell Jr A D., J. Chem. Theory Comput., 2015, 11(6): 2855-2867.).
Following the keyword BPCMAP, the integer NBTP integer indicates the
number of indvidual bpCMAPs that will be read. Each bpCMAP is then
specified individually as indicated by the LAMBDA value, the dimension
DIM of the map, the UNIT from which the specific bpCMAP is read and
the DIHEdrals to which the bpCMAP is being applied. Typically the
same value of lambda is used for each bpCMAP for a given replica
(though the current implementation allows this to be varied) and the
same bpCMAP can be read multiple times from the same UNIT. See the
example input below. Note that the bpCMAP energy is included with the
CMAPs energy reported in CHARMM. To access the bpCMAP energy
contribution an energy calculation without invoking bpCMAP must be
perfomed and the difference in the CMAPs energy term obtained.
NBTP [integer]: Number of bpCMAPs.
LAMBDA [real]: scaling factor of the biased potential CMAP: the default value is 1.d0 .
DIM [integer]: The dimensions of the specific bpCMAP: the default value is 24.
UNIT [integer]: The previously opened bpCMAP UNIT number.
DIHE: Specify the two dihedrals to which the bpCMAP is being
applied. 8x[atom_selection]. Note that each atom selection should only
select one atom.
END: to finish reading bpCMAPs
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Examples of MMFP GEO subcommnads
1) To setup a harmonic spherical restraint on all oxygens around the origin
(by default is harmonic potential and a sphere centered at the origin)
MMFP
GEO force 100.0 select type O* end
END
The entirely equivalent detailed command would be
MMFP
GEO sphere harm xref 0.0 yref 0.0 zref 0.0 force 100.0 select type O* end
END
2) The spherical quartic potential is very similarly to SBOUND potential
(Suitable for a sphere of radius of 13.0 angstroms centered at the origin)
MMFP
GEO sphere quartic -
force 0.2 droff 13.0 p1 2.25 select type OH2 end
END
3) To impose a harmonic restraint on the center of mass of carbon alpha around
(x,y,z) = (1.0,2.0,3.0)
MMFP
GEO sphere RCM -
xref 1.0 yref 2.0 zref 3.0 -
force 10.0 droff 0.0 select type CA end
END
4) To apply a harmonic cylindrical tube constraint of 8 angstroms radius,
the axis of the cylinder is directed along ydir 1.0 and passes through the
point: xref=4.0,yref=5.0,z=6.0)
MMFP
GEO cylinder -
xref 4.0 yref 5.0 zref 6.0 xdir 0.0 ydir 1.0 -
force 100.0 droff 8.0 select type CA end
END
5) To apply a planar harmonic constraint with normal in zdir 1.0
MMFP
GEO plane -
xref 7.0 yref 8.0 zref 9.0 zdir 1.0 -
force 100.0 droff 0.0 select type N* end
END
6) To fix the distance between the center of mass of two subset of atoms
(e.g., two domains of a protein, two amino acids, etc...)
MMFP
GEO sphere RCM distance -
harmonic symmetric force 10.0 droff 5.0 -
select bynu 1:10 end select bynu 11:20 end
END
7) To constrain the distance along an axis vector joining the center of mass
of two subset of atoms
(e.g., and ion between two domains of a protein, two amino acids, etc...)
MMFP
GEO ADIStance sphere RCM SELE RESName POT end -
harmonic symmetric force 10.0 droff 5.0 -
select bynu 1:10 end select bynu 11:20 end
END
8) To constrain the angle between the center of mass of 3 subset of atoms
(e.g., 3 domains of a protein, 3 amino acids, etc...)
MMFP
GEO sphere RCM angle -
harmonic symmetric force 1000.0 tref 5.0 dtoff 0.0 -
select bynu 1:10 end select bynu 11:20 end select bynu 21:30 end
END
Thus, the TREF variable specifies the reference angle value while the DTOFF
variable specifies the offset to be used if necessary.
The previous implementation (till c30 version) used DROFF to specify reference
angle/dihedral value with no provision for specifying flat-bottom harmonic
potential with an offset, the previous command is still valid but is not
recommended.
9) To constrain the dihedral angle between the center of mass of 4 subset of
atoms (e.g., 4 domains of a protein, 4 amino acids, etc...)
MMFP
GEO sphere RCM dihedral -
harmonic symmetric force 1000.0 tref 5.0 dtoff 0.0 -
select bynu 1:10 end select bynu 11:20 end -
select bynu 21:30 end select bynu 31:40 end
END
10) In using VMOD to constrain the system to a given mrms value along a
normal mode, the modes must have been calculated previously and the binary
file opened for reading before entering the MMFP facility. Further, when
the initialization command is given the current coordinates must be those
of the minimum-energy configuration used for the mode calculation.
To restrain the system to an mrms value of 0.1 along the first vibrational
mode (mode 7), the following sequence is appropriate:
MMFP
VMOD INIT MXMD 1 KROT 1000 KCGR 1000 UMDN 10 UOUT 11 NSVQ 10
VMOD IMDN 7 KMDN 100 QN 0.1
END
Force constants must of course be adapted to the problem at hand.
11) To reset all GEO potentials to zero and deallocate the HEAP space
MMFP
GEO reset
END
12) To use the PHS method (BHEL and SHELL commands) to run constant pressure
simulations in which the protein is solvated only by a thin shell of water
MMFP
BHEL SELE .not. (resname TIP3 .or. hydrogen) END
SHEL SELE (resname tip3 .and. type oh2) end DRSH 8.0 RWEL 0.25 PFINAL 1.0
SCO 0 RELA 0.00001 UPDF 10 CHFR 1000 SPACE 1000000 CHCO 0.00001 FOCO1 3 FOCO2 15 CUT 2
END
13) To use the RE method by using the EPR Key word, it is required to have the
EPR/DEER distance distributions. A typical EPR/DEER file can be called by the
following command:
open read card unit 50 name epr_constraints.dat
The epr_constraints.dat file contains all the experimental spin-pair distance
distributions. First, the two spin-label residue numbers must be written which
is followed by the corresponding EPR/DEER distance distribution.The distributions
must be normalized to 1. Bin spacing must be equal for all the bins and must be
same as in the DELPPP. The Number of spin-pair distributions and the total number
of bins in the EPR/DEER histogram must be same as in the NPTOT and NPPP.
An example of the charmm commands for the RE simulation is as follows:
MMFP
EPR NSPINLABELS 5 NREPLICA 25 KENPP 10000 SIG2EPR 1.7 -
select type ON .and. resnam CYR1 end -
DELPPP 1.0 NPTOT 3 NPPP 70 UNIT 50 VERBOSE
END
In the above example, there are 5 spin-labels each of which are replicated 25 times.
There are 3 EPR/DEER distributions with a total of 70 bins each with a bin spacing of
1.0 Angstrom. A force constant of 10000 (kcal/mol) is used for the energy restraint.
An example of the CHARMM commands to apply BPCMAPs to a simulation of
polypeptide follows. Note that the same bpcmaps could be read for
each set of dihedrals by specifying the same UNIT number.
open read unit 30 card name cmap_1.bpcmap
open read unit 31 card name cmap_2.bpcmap
open read unit 32 card name cmap_3.bpcmap
MMFP
BPCMAP NBTP 3
LAMBDA 0.5 DIM 24 UNIT 30 DIH -
select atom proa 1 CY end select atom proa 1 N end -
select atom proa 1 CA end select atom proa 1 C end -
select atom proa 1 N end select atom proa 1 CA end -
select atom proa 1 C end select atom proa 2 N end
LAMBDA 0.5 DIM 24 UNIT 31 DIH -
select atom proa 1 N end select atom proa 1 CA end -
select atom proa 1 C end select atom proa 2 N end -
select atom proa 1 CA end select atom proa 1 C end -
select atom proa 2 N end select atom proa 2 CA end
LAMBDA 0.5 DIM 24 UNIT 32 DIH -
select atom proa 2 N end select atom proa 2 CA end -
select atom proa 2 C end select atom proa 2 NT end -
select atom proa 2 CA end select atom proa 2 C end -
select atom proa 2 NT end select atom proa 2 CAT end
END
14) Set up a FIRES potential for adaptive QM/MM simulations.
Select the water molecules near a copper ion (resname cuii) as the inner region (segid meta),
the other water as outer region. The potential is computed relative to the position
of the Cu(II) ion (reference).
define bslv sele .byres. (resn tip3 .and. .not. (segid meta)) end
! ...... set up FIRES ......
open write form unit 80 name @d@j_d16_fires.dat
mmfp
geo sphere harm RMAX force 100.0 -
select (resname cuii) end - ! reference point for FIRES
select (segid meta .and. type OH2) end - ! inner water
select (bslv .and. type OH2) end - ! outer water
iummfp 80
end
Examples of MMFP GEO subcommnads
1) To setup a harmonic spherical restraint on all oxygens around the origin
(by default is harmonic potential and a sphere centered at the origin)
MMFP
GEO force 100.0 select type O* end
END
The entirely equivalent detailed command would be
MMFP
GEO sphere harm xref 0.0 yref 0.0 zref 0.0 force 100.0 select type O* end
END
2) The spherical quartic potential is very similarly to SBOUND potential
(Suitable for a sphere of radius of 13.0 angstroms centered at the origin)
MMFP
GEO sphere quartic -
force 0.2 droff 13.0 p1 2.25 select type OH2 end
END
3) To impose a harmonic restraint on the center of mass of carbon alpha around
(x,y,z) = (1.0,2.0,3.0)
MMFP
GEO sphere RCM -
xref 1.0 yref 2.0 zref 3.0 -
force 10.0 droff 0.0 select type CA end
END
4) To apply a harmonic cylindrical tube constraint of 8 angstroms radius,
the axis of the cylinder is directed along ydir 1.0 and passes through the
point: xref=4.0,yref=5.0,z=6.0)
MMFP
GEO cylinder -
xref 4.0 yref 5.0 zref 6.0 xdir 0.0 ydir 1.0 -
force 100.0 droff 8.0 select type CA end
END
5) To apply a planar harmonic constraint with normal in zdir 1.0
MMFP
GEO plane -
xref 7.0 yref 8.0 zref 9.0 zdir 1.0 -
force 100.0 droff 0.0 select type N* end
END
6) To fix the distance between the center of mass of two subset of atoms
(e.g., two domains of a protein, two amino acids, etc...)
MMFP
GEO sphere RCM distance -
harmonic symmetric force 10.0 droff 5.0 -
select bynu 1:10 end select bynu 11:20 end
END
7) To constrain the distance along an axis vector joining the center of mass
of two subset of atoms
(e.g., and ion between two domains of a protein, two amino acids, etc...)
MMFP
GEO ADIStance sphere RCM SELE RESName POT end -
harmonic symmetric force 10.0 droff 5.0 -
select bynu 1:10 end select bynu 11:20 end
END
8) To constrain the angle between the center of mass of 3 subset of atoms
(e.g., 3 domains of a protein, 3 amino acids, etc...)
MMFP
GEO sphere RCM angle -
harmonic symmetric force 1000.0 tref 5.0 dtoff 0.0 -
select bynu 1:10 end select bynu 11:20 end select bynu 21:30 end
END
Thus, the TREF variable specifies the reference angle value while the DTOFF
variable specifies the offset to be used if necessary.
The previous implementation (till c30 version) used DROFF to specify reference
angle/dihedral value with no provision for specifying flat-bottom harmonic
potential with an offset, the previous command is still valid but is not
recommended.
9) To constrain the dihedral angle between the center of mass of 4 subset of
atoms (e.g., 4 domains of a protein, 4 amino acids, etc...)
MMFP
GEO sphere RCM dihedral -
harmonic symmetric force 1000.0 tref 5.0 dtoff 0.0 -
select bynu 1:10 end select bynu 11:20 end -
select bynu 21:30 end select bynu 31:40 end
END
10) In using VMOD to constrain the system to a given mrms value along a
normal mode, the modes must have been calculated previously and the binary
file opened for reading before entering the MMFP facility. Further, when
the initialization command is given the current coordinates must be those
of the minimum-energy configuration used for the mode calculation.
To restrain the system to an mrms value of 0.1 along the first vibrational
mode (mode 7), the following sequence is appropriate:
MMFP
VMOD INIT MXMD 1 KROT 1000 KCGR 1000 UMDN 10 UOUT 11 NSVQ 10
VMOD IMDN 7 KMDN 100 QN 0.1
END
Force constants must of course be adapted to the problem at hand.
11) To reset all GEO potentials to zero and deallocate the HEAP space
MMFP
GEO reset
END
12) To use the PHS method (BHEL and SHELL commands) to run constant pressure
simulations in which the protein is solvated only by a thin shell of water
MMFP
BHEL SELE .not. (resname TIP3 .or. hydrogen) END
SHEL SELE (resname tip3 .and. type oh2) end DRSH 8.0 RWEL 0.25 PFINAL 1.0
SCO 0 RELA 0.00001 UPDF 10 CHFR 1000 SPACE 1000000 CHCO 0.00001 FOCO1 3 FOCO2 15 CUT 2
END
13) To use the RE method by using the EPR Key word, it is required to have the
EPR/DEER distance distributions. A typical EPR/DEER file can be called by the
following command:
open read card unit 50 name epr_constraints.dat
The epr_constraints.dat file contains all the experimental spin-pair distance
distributions. First, the two spin-label residue numbers must be written which
is followed by the corresponding EPR/DEER distance distribution.The distributions
must be normalized to 1. Bin spacing must be equal for all the bins and must be
same as in the DELPPP. The Number of spin-pair distributions and the total number
of bins in the EPR/DEER histogram must be same as in the NPTOT and NPPP.
An example of the charmm commands for the RE simulation is as follows:
MMFP
EPR NSPINLABELS 5 NREPLICA 25 KENPP 10000 SIG2EPR 1.7 -
select type ON .and. resnam CYR1 end -
DELPPP 1.0 NPTOT 3 NPPP 70 UNIT 50 VERBOSE
END
In the above example, there are 5 spin-labels each of which are replicated 25 times.
There are 3 EPR/DEER distributions with a total of 70 bins each with a bin spacing of
1.0 Angstrom. A force constant of 10000 (kcal/mol) is used for the energy restraint.
An example of the CHARMM commands to apply BPCMAPs to a simulation of
polypeptide follows. Note that the same bpcmaps could be read for
each set of dihedrals by specifying the same UNIT number.
open read unit 30 card name cmap_1.bpcmap
open read unit 31 card name cmap_2.bpcmap
open read unit 32 card name cmap_3.bpcmap
MMFP
BPCMAP NBTP 3
LAMBDA 0.5 DIM 24 UNIT 30 DIH -
select atom proa 1 CY end select atom proa 1 N end -
select atom proa 1 CA end select atom proa 1 C end -
select atom proa 1 N end select atom proa 1 CA end -
select atom proa 1 C end select atom proa 2 N end
LAMBDA 0.5 DIM 24 UNIT 31 DIH -
select atom proa 1 N end select atom proa 1 CA end -
select atom proa 1 C end select atom proa 2 N end -
select atom proa 1 CA end select atom proa 1 C end -
select atom proa 2 N end select atom proa 2 CA end
LAMBDA 0.5 DIM 24 UNIT 32 DIH -
select atom proa 2 N end select atom proa 2 CA end -
select atom proa 2 C end select atom proa 2 NT end -
select atom proa 2 CA end select atom proa 2 C end -
select atom proa 2 NT end select atom proa 2 CAT end
END
14) Set up a FIRES potential for adaptive QM/MM simulations.
Select the water molecules near a copper ion (resname cuii) as the inner region (segid meta),
the other water as outer region. The potential is computed relative to the position
of the Cu(II) ion (reference).
define bslv sele .byres. (resn tip3 .and. .not. (segid meta)) end
! ...... set up FIRES ......
open write form unit 80 name @d@j_d16_fires.dat
mmfp
geo sphere harm RMAX force 100.0 -
select (resname cuii) end - ! reference point for FIRES
select (segid meta .and. type OH2) end - ! inner water
select (bslv .and. type OH2) end - ! outer water
iummfp 80
end
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MMFP Substitution Parameters
There are several different variables that can be substituted in
titles or CHARMM commands that are set by some of the MMFP commands
(*note doc/miscom.info). Here is a summary and description of each variable.
----------------------------------------------------------------------------
'GEO'
The total energy contribution of the GEO restraining potentials.
----------------------------------------------------------------------------
'XCM','YCM','ZCM'
The position of the center of mass of the last set of atom is returned.
----------------------------------------------------------------------------
'XCM2','YCM2','ZCM2'
The position of the center of mass of the second set of atoms is
returned if the key word DISTANCE ADISTANCE or ANGLE or DIHEDRAL was issued.
----------------------------------------------------------------------------
'XCM3','YCM3','ZCM3'
The position of the center of mass of the third set of atoms is
returned if the key word ADISTANCE, ANGLE or DIHEDRAL was issued.
----------------------------------------------------------------------------
'XCM4','YCM4','ZCM4'
The position of the center of mass of the fourth set of atoms is
returned if the key word DIHEDRAL was issued.
----------------------------------------------------------------------------
'RGEO'
The distance/angle/dihedral used in the last potential calculation
is returned. Set if a MMFP constraint with the keyword DIST, ADIS or
ANGLE or DIHEDRAL was used.
----------------------------------------------------------------------------
'RADI'
The instantaneous sphere radius for the SSBP method.
----------------------------------------------------------------------------
'SSBPLRC'
long-range free energy correction for SSBP. Only set in PERT
calculation with SSBP
----------------------------------------------------------------------------
'SSBPLRCS'
standard deviation of SSBP long-range correction. Only set in PERT
calculation with SSBP
----------------------------------------------------------------------------
'DRSH'
The thickness of the water shell in the PHS method (SHELL key word)
----------------------------------------------------------------------------
'SCO'
The ratio of the outward and inward external forces in the PHS method
(SHELL key word).
----------------------------------------------------------------------------
Future developments:
1. The SSBP potential will be implemented for active site solvation (in
which a large part of the protein lies outside the spherical region).
MMFP Substitution Parameters
There are several different variables that can be substituted in
titles or CHARMM commands that are set by some of the MMFP commands
(*note doc/miscom.info). Here is a summary and description of each variable.
----------------------------------------------------------------------------
'GEO'
The total energy contribution of the GEO restraining potentials.
----------------------------------------------------------------------------
'XCM','YCM','ZCM'
The position of the center of mass of the last set of atom is returned.
----------------------------------------------------------------------------
'XCM2','YCM2','ZCM2'
The position of the center of mass of the second set of atoms is
returned if the key word DISTANCE ADISTANCE or ANGLE or DIHEDRAL was issued.
----------------------------------------------------------------------------
'XCM3','YCM3','ZCM3'
The position of the center of mass of the third set of atoms is
returned if the key word ADISTANCE, ANGLE or DIHEDRAL was issued.
----------------------------------------------------------------------------
'XCM4','YCM4','ZCM4'
The position of the center of mass of the fourth set of atoms is
returned if the key word DIHEDRAL was issued.
----------------------------------------------------------------------------
'RGEO'
The distance/angle/dihedral used in the last potential calculation
is returned. Set if a MMFP constraint with the keyword DIST, ADIS or
ANGLE or DIHEDRAL was used.
----------------------------------------------------------------------------
'RADI'
The instantaneous sphere radius for the SSBP method.
----------------------------------------------------------------------------
'SSBPLRC'
long-range free energy correction for SSBP. Only set in PERT
calculation with SSBP
----------------------------------------------------------------------------
'SSBPLRCS'
standard deviation of SSBP long-range correction. Only set in PERT
calculation with SSBP
----------------------------------------------------------------------------
'DRSH'
The thickness of the water shell in the PHS method (SHELL key word)
----------------------------------------------------------------------------
'SCO'
The ratio of the outward and inward external forces in the PHS method
(SHELL key word).
----------------------------------------------------------------------------
Future developments:
1. The SSBP potential will be implemented for active site solvation (in
which a large part of the protein lies outside the spherical region).