SDA7 input file format
The input file consists of a series of grouped input
parameters, delimited by the keyword GROUP
GROUP = groupname
...
END GROUP
and a list of free parameters which are not associated with
a group.
All input parameters have the following form :
name-of-parameter
= parameter-value
Lines begining with the character "#" or "!" are treated as
comment lines and will not be parsed by the program.
Note: do not insert spaces in front of "#" if you want to
comment out a line!
Example input files
Detailed description of the input parameters
GROUP =
Type_Calculation:
type, total_solutes,
total_grids
-
type
[string]
(sda_2proteins)
: type of calculation -
defines which type of calculation will be performed.
The following options are available:
-
sda_2proteins
: for docking,
association rate calculation or electron
transfer
-
sdamm
: simulation with
multiple proteins.
-
sda_koff
: k_off
calculation.
-
sda_energy
: compute interaction
energy from complexes or trajectory files.
-
total_solutes [integer] (2) : total number of solutes
-
total_grids [integer] (2) : total number of grids (if a solute
has more than one grid to account for
conformational/structural variation, this only counts
as 1 grid ). In fact, the number of set_of_grids =
number of GROUP Solute_Grid
GROUP = Reaction
Criteria:
computation, rxna12f,
et_sol1, et_sol2, dind, nnnons, nwrec
-
computation [string] (off_rc) : define which type of simulation is
being performed. Options:
-
association
: compute association
rate at every distance and for any number of
contacts defined in group RateCalculation. Use
*.rxna file and dind to define the criteria and
their independence, all criteria are considered as
nonspecific.
-
docking
: a complex must
satisfy all specific criteria and at least nnnons
non-specific ones in order to be saved in the
complexes file
-
electron_transfer
: compute elctron
transfer. The reaction criteria are read from 2
input files ( et_sol1 and et_sol2 )
-
all
: all complexes are
saved to the complexes file. No checks are
performed
-
off_rc
: disactivate the
reaction criteria module, no calculations
performed
-
rxna12f [string] (prot12.rxna) : filename for the reaction criteria
used for docking or association rate
calculations.
Input examples for barnase-barstar docking
and association
rates are available in the examples.
Reaction atoms do not have to be real atoms, although
in this file these atoms/points should be given like
atoms in PDB format. Different combinations of
the same atoms/points can be prepared by editing these
reaction atom files
-
et_sol1, et_sol2 [string] (empty) : filenames for the reaction criteria
for electron transfer calculations. Files must be
generated with the Harlem software.
-
dind
[float] (6.) : minimal distance (in Å) between atoms
on the same solute defining contacts for satisfying
reaction criteria (equivalent to d_min in figure
below)
-
nnnons [integer] (2) : minimum number of nonspecific
constraints to satisfy to define an encounter
complex
-
nwrec [integer] (0) : number of the window up to which the
complexes are recorded. For example, in the
situation below, nwin=5 reaction
distance windows are defined, and rates for forming
contacts at each of these 5 distances will be
monitored. Encounter complexes with contact
distances less than
win0+dwin*(nwrec-1), will be
recorded.
Reaction criteria are used to define a "complex" between
2 solutes. Full freedom is let to the user:
- Define a center-to-center distance criteria between
the solutes, usually for docking
- A set of donor-acceptor pairs from an initial
complex, needed for association rates
- Any other constraints suitable with experimental
data: distance between 2 atoms satisfying crosslink
experiments, FRAP or FRET data, known interactions with a
specific residue / ligand...
- All constraints can be freely combined
The list of reaction criteria must be provided in a
separate file (conventionally named with a suffix
*.rxna), where the fields indicate:
- The keyword for the type of reaction criteria
(discussed below)
- The position of the atom of the solute 1 (the atom
number is needed in the case of a flexible solute)
- The minimum distance that the 2 reaction criteria
must satisfy
- The position of the atom of the solute 2 (the atom
number is needed in the case of a flexible solute)
For docking, there are 3 different types of reaction you
can use:
- CSPEC: specific constraint, this reaction criterion
must be satisfied for the complex to be accepted
- CNONS: nonspecific constraint, at least
nnnons of these reaction criteria must
be satisfied
- ASPEC: anti-specific, this criterion must be invalid
(new in SDA 7)
For association rate calculations, all entries in the
*.rxna file are considered as CNONS. But you can still
record complexes and adjust the nwrec
input parameter.
To get the specific format of the *.rxna file, we advise
you to look at the input files in the barnase-barstar
example of docking. Here are illustrated:
- A blind simulation, where only the center to
center distance between the protein is used as a
criterion
- An example where the center-to-center distance
criterion is used together with nonspecific reaction
criteria
Or you can refer to the technical documentation,
linked here in the
section Reaction Criteria.
(The doxygen documentation must be generated before using
this link).
Usage of dind
To avoid an artificially large number of contacts, the
variable dind can be used.
On the figure below, all atoms used in the reaction
criteria are represented by spheres. But only those which
are at a separation greater than d_min are considered as
independent (black spheres). So with this schema, there
will be a maximum of 4 independent contacts.
GROUP =
RateCalculation:
win0, nwin, dwin,
nb_contact, bootstrap, fpt
-
win0
[float] (3.0) : reaction distance window minimum
value (in Å)
-
nwin
[integer]
(0) : number of reaction distance
windows.
-
dwin
[float] (0.5) : reaction distance window step (in
Å).
-
-
nb_contact [integer] (4) : maximum number of pair contacts to be
considered. This parameter is only applicable for
association rate calculations.
-
bootstrap [bool] (0) : if 1, association rates and first
passage time results are printed for every trajectory.
Final results can be computed with bootstraping
(auxi/bootstrap.py)
-
fpt
[bool] (0) if 1, record the first passage time, if
bootstrap==1 same processing with
(auxi/bootstrap.py)
GROUP =
Analytical:
h_analytic, debyeh, ionic_strength, hydrodynamic
-
h_analytic
[float] (0.01) : defines the bin size (in Å) of the precomputed arrays
-
debyeh
[bool] (0) : if 1, activates debye-huckel interactions for all solutes
-
ionic_strength
[float] (0.150) : if debye-huckel, specifies the ionic strength (in Molar)
-
hydrodynamic
[bool] (0) : if 1, activates hydrodynamics interactions for all solutes
-
lvol_rcut
[float] (0.0) : defines the local volume radius if hydrodynamics interactions are used. Must be greater than the largest Stokes radius of any solute in the system.
GROUP =
Solute_Grid:
nb_solute, pdb_filename,
diffusion_trans, diffusion_rotat, rotate, surface, flex,
epf, qef, edf, hdf, ljf, lj_repf, nb_lj, atom_lj,
list_conformation, stoke_radius, total_conf, method,
initial_conf, frequency, std_frequency
-
nb_solute [integer] (1) : number of identical solutes ( of the
same type)
-
pdb_filename [string] (empty) : name of pdb file for this group of
solutes
-
diffusion_trans [float] (0.0123) : absolute translational diffusion
coefficient in Å2/ps. In the case of
sda_2proteins, the translational diffusion constant of
solute 2 should be assigned as the sum of the diffusion
coefficients of solute 1 + solute 2 to simulate the
relative translational diffusion.
According to the Einstein-Stokes formula, the
translational diffusion constant scales inverse
proportionally to the solvent viscosity (which itself
has a complicated dependence on the temperature), and
inverse proportionally to the (hydrodynamic) radius of
a solute. 1 Å2/ps = 10-8
m2/s = 10-4
cm2/s
-
diffusion_rotat [float] (1.36e-4) : rotational diffusion coefficient of
the solute in radian2/ps. This is inversely
proportional to the square of the solute radius.
diffusional_rotat is inversely
proportional to the solvent viscosity. For lysozyme,
for example, dr=2.6*10-5
radian2/ps.
-
rotate [bool] (1) : switch to define whether the solute
rotates. 0 means no rotation and
diffusion_rotat is not used. 1 means
the solute can rotate and
diffusion_rotat is used.
-
surface [bool] (0) : switch to define whether this solute
is a surface. Being treated as a surface will influence
the distance computation and periodic boundary
conditions, and rotate will be set to
0 for this solute
-
flex
[bool] (0) : define if this solute(s) is flexible
(i.e. has more than 1 structure/conformation) or
not
-
image_charge [bool] (0) : define if the electrostatic image
charge of this solute(s) must be computed. It is
relevant in the case that one solute is a metal
surface.
-
stoke_radius [float] (0.) : if > 0, indicates the stoke_radius
for hydrodynamic interactions
-
Hydrodynamic interactions are implemented with
the Weinstein method, where the diffusion coefficients
are rescaled during the trajectory depending on the
instantaneous local volume fraction of solutes around
one solute. The infinite dilution values of the
diffusion coefficients can be obtained from the
HYDROPRO program, for instance, or determined from
experiments. See Mereghetti et al. (2012)in
references
-
epf
[string]
(empty)
: filename for the
electrostatic potential of the solute in UHBD binary
format. It is assumed that the potentials are
written in kcal/mol/e units. Note that APBS
generated grids written in UHBD format are in units of
kT/e and ascii and as such cannot be used directly with
SDA. They should be rescaled and converted with
the auxiliary program convert_grid, to bring them
into consistency with UHBD format.
-
qef
[string]
(empty)
: filename for effective
charges of the solute. This is the output of the
ECM suite program. See
detailed description in the faq
-
edf
[string]
(empty)
: filename for the
electrostatic desolvation potential of the solute in
UHBD format. This grid can be calculated with the
program make_epedhdlj_grd
which is included in the SDA distribution (units in
kcal/mol/e).
-
hdf
[string]
(empty)
: filename for the
hydrophobic desolvation potential of the solute in UHBD
format. This grid can be calculated with the program
make_epedhdlj_grd which is
included in the SDA distribution.
-
lj_repf [string] (empty) : filename for the soft-core repulsion
(approx. repulsive term of Lennard-Jones) grid of the
solute in UHBD format. It is intended to be used with
sdamm only where it replaces the use of the exclusion
grid. This grid can be calculated with the program
make_epedhdlj_grd which is
included in the SDA distribution.
-
nb_lj [integer] (0) : define the number of Lennard-Jones
potential grids. Used for the implementation of the
ProMetCS force field.
-
ljf
[array of string]
(empty)
: filenames for the
Lennard-Jones potential grids of the solute in UHBD
format. This grid needs an additional tool to be
computed
-
atom_lj [array of string] (empty) : atom names for the Lennard-Jones
interactions. If an unusual atom name, use the
"add_atoms" file to define the sites of
interaction.
-
These variables are only needed in the case where
the flag flex is set to 1
-
list_conformation
[string]
(empty)
: filename of the file
which defines multiple conformations/structures for a
solute. Every GROUP SoluteGrid may have a different
list.
-
total_conf [integer] (0) : define the total number of
conformations/structures, if this solute is treated as
flexible
-
method [string] (empty) : choose between the methods
implemented for changing conformations/structures.
Available options are:
-
-
random
: Choose a random
conformation (depending on nearest
input). The same conformation can be chosen.
Energies are not evaluated
-
minimum
: Implemented only with
nearest=1. The minimum energy
between the actual and the closest conformations (1
or 2 ) is selected
-
metropolis
: The potential energy
in the initial conformation (E0) is computed. For a
random chosen conformation ( depending on
nearest ), the new energy (E1) is
computed and the move is accepted if:
-
-
the new
conformation has a lower energy: E1 is less
than E0, or
-
a random number
uniformly generated in the range [0,1] is lower
than exp(E1-E0)
-
nearest [bool] (0) : If 1, moves are limited to the
nearest neighbour ( conformation +/- 1). It is used
with conformations from normal mode analysis for
instance.
Otherwise a random conformation is chosen (used with
NMR structures). The same conformation can be
selected.
-
initial_conf [integer] (1) : Specify the conformation chosen at
the beginning of every trajectory.
-1 makes a random choice
-
frequency [float] (100) : Specify the delay between the changes
in conformation (in ps). The delay is computed as a
Gaussian random number with average
frequency and standard deviation
std_frequency.
-
std_frequency [float] (0) : Specify the standard deviation (in
ps). Used in the case of SDAMM to avoid synchronisation
between the solutes.
GROUP =
Geometry:
type, pbc, surface, escape,
start_position, c_surface, min_X, max_X
-
type [string] (sphere) : specify the geometry of the
simulation box
-
sphere :
: Use a spherical geometry,
only for use with sda_2proteins types of
simulation
-
box :
: Use a box for simulation,
only for use with sda_2proteins types of simulation
(protein-surface case) and with sdamm
-
pbc
[bool] (0) : Switch on Periodic Boundary
Conditions. Apply only with a box geometry
-
surface [bool] (0) : Indicates if a surface is present in
the system. PBC rules are modified in this case. Can
also be used with a spherical geometry in sda_2proteins
simulations
-
escape [bool] (1) : Indicates if a solute can escape. The
trajectory is then stopped when the solute reaches the
c_surface (with a sphere) or zmax (in a box)
-
start_pos [float] (100.) : Indicates the initial position (in Å)
of the second solute in sda_2proteins. Simulations are
started by placing the center of the second solute at
the distance start_position .
This corresponds to the b-surface for a spherical
geometry.
If surface is activated, the initial
position is generated on the upper-half of the
sphere.
For calculation of association constants, there should
be no interactions between the solutes at this
distance. With finite size grids,
start_position can be selected to be
larger than the sum of the solute 1 (or 2) grid extents
and the solute 2 (or 1) radius.
To check with box.
-
c
[float] (150.) : defines the c-surface (in Å) in the
case of a sphere
-
Xmin,Xmax
[float] (0.) : define the size of the box (in Å). If
escape is activated, zmax has the role
of the c-surface.
Typical setup for simulations within a sphere.
Trajectories are started at the b-surface
(start_pos) and finish when solute 2
goes through the c-surface (c).
GROUP =
Timestep:
variable,
dt1,
swd1,
dt2,
swd2
-
variable [bool] (1) : switch to a variable timestep ( in
sda_2proteins simulation), or to a fixed timestep
(sdamm) when the value of dt1 is
used
-
dt1
[float] (1.0) : basal simulation timestep (in ps,
picoseconds). This is the smallest timestep used
and is employed when the center-to-center separation is
less than swd1 or the distance at
which the solutes have the possibility to contact (i.e.
the center-to-center distance between solutes is less
than rhit = the sum of maximal extents
+ probe radius + maximal radius of solute 1
atoms).
-
swd1
[float] (50.0) : center-to-center distance (Å) at
which the timestep starts to increase
-
dt2
[float] (1.0) : timestep at distance
swd2
-
swd2
[float] (90.0) : center-to-center distance at which
timestep equals dt2.
-
rswd
[*] (*) : deprecated in SDA 7, the rotation of
solute2 is only proportional to the timestep
These parameters define the variable timestep designed to
accelerate simulations. As shown in the figure below, the
timestep is automatically decreased to zero near the
c-surface to reduce artifacts due to truncation of the
trajectories. Although the profile of the time step
influences the computed rates, the most important
parameter is dt1. Take care not to choose a too small
value for this parameter (since the computing time scales
almost linearly with it). The physical parameter
sqrt(dt*dm) measures an average Brownian dynamics step
length. This must be less than 1 Å, which is the
characteristic distance describing the roughness of any
protein surface since the atomic bond lengths and van der
Waals radii define this scale. Moreover, dt1 should be
less than the characteristic distance over which the
interaction forces vary substantially, which means that
the optimal value is influenced by interaction force
strength: one needs smaller time steps for stronger
interacting proteins. The standard output will print
additional information, like the location and the value
of the maximum timestep.
GROUP
= ResidenceTime:
type_residence,
fixed_bin_size, size_X,
cell_X,shift_rt_X,format_rt3d,pair_solutes
-
type_residence [string] (off) : can use different geometry
-
-
off
: default, disactivate
the module
-
distance
: record the
center-to-center distance between the
solutes
-
plan
: project on a
surface
-
resid_3d
: record on a 3d
grid
-
fixed_bin_size [integer: 0,1,2] (0) : adjust the size of the
arrays/grids
-
-
0
: the number of cells
is fixed (cell_X), adapt the size to fill up to the
c-surface
-
1
: fix the size of one
cell (size_x), adapt the size to fill up to the
c-surface
-
2
: fix both the number
of cells (cell_X) and the size of one cell (size_X)
to allow to focus on the solute 1
-
size_x, size_y, size_z : size of each cell (in Å), the UHBD
format allows only an identical spacing for
visualisation
-
cell_x, cell_y, cell_z : number of cells in each
direction
GROUP =
Complexes:
fcomplexes,
restart_complex,
binary_complex,
nb_complexes,
rmsd_min,
ionerun,
complex_sum_energy
merge_step,
size_thread,
ftrajectories,
binary_trajectory,
ntraj_rec,
freq_print,
trajectory_sum_energy,
max_array_traj
-
fcomplexes [string] (empty) : filename to record output complexes.
By default this is switched off, no complexes are
recorded.
-
restart_complex [bool] (0) : If switched on, the complex file will
be first read during the initialisation. This is used
in the case that we want to continue a simulation. Note
that it is important to change the random number
generator seed, otherwise you may reproduce identical
trajectories.
-
binary_complex [bool] (0) : Switch to choose between ascii or
binary output format. Ascii files are human readable,
but binary improves the precision of the numbers.
binary may also save disk space, but this is relatively
limited. Default is ascii.
-
nb_complexes [integer] (500) : No. of distinct lowest energy
configurations to write. Complexes with a higher energy
are discarded
-
rmsd_min [float] (2.0) : minimum rmsd between complexes in Å.
During the BD simulations, if a new docking pose is
considered similar to a previously stored pose, then
the configuration with the lowest total energy is
stored and the counter for this docking pose is
increased. A pose is considered similar to a previous
pose if they have an RMSD less than the designated
threshold
-
ionerun [bool] (0) : Switch to choose whether rmsd values
are compared with other trajectories (if ionerun = 0)
or only compared within individual trajectory (if
ionerun = 1)
-
complex_sum_energy
[bool] (0) : Switch to choose the format of the
energy terms. If set to zero ( default ) the energy
components are split into the energy of the solute 1 in
the grid of the solute 2 and its inverse. If set to 1,
only the sum is printed out. We expect the
electrostatic energy terms to be similar. Due to the
approximation in the PB calculations, grids and
effective charges the energies cannot be exactly the
same, but should be approximately the same.. If a
difference of a factor of more than 2 occurs, this may
indicate an inadequate electrostatic and/or effective
charge calculation.
-
merge_step [integer] (input dependent)
: In case of OpenMP only,
indicate how often every thread merges their complexes
into a global complexes file. The default values are
chosen from different parameters in the input
file.
-
size_thread [integer] (input dependent)
: In case of OpenMP only,
indicate the size of the complexes list of each
thread.
-
ftrajectories [string] (empty) : filename to record the trajectory
output. By default this is switched off and no
trajectory is recorded.
-
binary_trajectory [bool] (0) : Switch to choose between ascii or
binary output format. Ascii files are human readable,
but binary improves the precision of the numbers. The
effect on the number precision is clearly seen in the
case of a sdamm trajectory. If set to 1, the restart
file will also be saved in binary format. Binary may
also save disk space, but this is relatively limited.
Default is ascii.
-
ntraj_rec [integer] (-1) : trajectory no. to be recorded. If the
value is negative, all trajectories will be recorded.
If the value = 0, no trajectories will be recorded. If
the value is positive, record only this trajectory
number.
-
freq_print [integer] (100) : frequency ( in steps ) with which the
conformations are recorded in the trajectory
file.
-
trajectory_sum_energy
[bool] (0) : Like complex_sum_nrj
for the trajectory. The algorithm is written to apply
with any number of types.
-
max_array_traj [integer] (nb. of solutes) : Maximum size of the array for the
trajectory. The array is printed to file when
filled.
GROUP =
MetalDesolvation:
distance_to_surface,
energy_per_water, radius_patch, radius_water
- This energy term has been
parametrized for computing Au(111)-protein interaction
energies. Computation of forces has not been
parameterized:
-
distance_to_surface
[float] (6.5) : in Å (Zadw); the position of the
first hydration layer (3 Å) plus the average LJ radius
of protein-surface interaction
-
energy_per_water [float] (0.13) : Φ°_metd in kT/Ų ; desolvation energy
per unit area of the first hydration
layer
-
radius_patch [float] (6.0) : α in Å; (aadw) parameter for
calculation of the surface desolvation potential Φ as
parametrized from MD simulations of PMF for the test
atom on the Au(111) surface
-
radius_water [float] (1.5) : Radw in Å; The effective desolvation
radius that defines the surface area each protein atom
is assumed to desolvate.
The surface desolvation energy is calculated as :
The computed desolvated area is shown by bold lines, the
solid and dashed lines corresponding to water desorption
from the first and second hydration layers, respectively.
The circles with crosses represent close solute atoms and
that with a zero is at an intermediate distance.
GROUP =
PMF:
mentth, mentfi, mentom, mentx, menty, pstart,
pfinish, dz
- Potential of mean force (PMF) calculations
is based on a thermodynamic integration method where
configurational space of the protein is sampled over the euler angles
(θ, ϕ, ω) and a number
of dx,dy and dz coordinates based on the parameters:
-
mentth
[integer] (60) : Number of θ angles to be explored in rotational sampling.
The angles range between 0 and π with a stepwise incrementation (π ÷ (mentth - 1))
-
mentfi
[integer] (120) : Number of ϕ angles to be explored in rotational sampling.
The angles range between 0 and 2π with a stepwise incrementation (2π ÷ (mentfi - 1))
-
mentom
[integer] (60) : Number of ω angles to be explored in rotational sampling.
The angles range between 0 and 2π with a stepwise incrementation (2π ÷ (mentom - 1))
-
mentx
[integer] (6) : Number of subdivisions (dx) of the surface along the x axis to be sampled.
The sampling length in the x direction is 6 Å
-
menty
[integer] (6) : Number of subdivisions (dy) of the surface along the y axis to be sampled.
The sampling length in the y direction is 6 Å
-
pstart
[float] (0.0) : Starting distance of the center of geometry of the protein from the surface in Å
-
pfinish
[float] (60.0) : Finishing distance of the center of geometry of the protein from the surface in Å
-
dz
[float] (0.2) : Incrementation length along z axis in Å
Parameters not associated with a group, they apply to all
solutes
-
dseed [float] (256.) : random number generator seed. If the
value is 0, it uses the time clock. With OpenMP, it is
not guaranteed that the same trajectory will be
obtained with the same seed.
-
nrun
[integer]
(1) : number of trajectories to generate.
Only 1 is possible with SDAMM. The higher this number,
the higher is the number of reactive trajectories
(nrun_reactive). The relative error of the calculated
rate constant is ~ 1/sqrt(nrun_reactive). This means
that to have the same relative error, a larger value of
nrun is required in cases with lower association rate
constants.
-
timemax [float] (0.) : = maximum length of computed
trajectories in ps (only incremented when the distance
between the solutes is smaller than rhit).
If timemax = 0, there is no limit; recommended for
association rate calculations.
-
nprint : deprecated; frequency with
which rate of information is printed: the fraction of
reactive trajectories is printed every nprint
runs. This is most useful when the simulation
takes a long time, then intermediate results are
available after each nprint trajectories.
Values of the different probes
-
probep [float] (1.7) : radius of the probe representing the
surface atoms of the solutes. Namely, proteins are
represented as a collection of atoms with solvent
accessibility larger than threshold
and each of these atoms is assigned a radius of
probep (Å). Typical values of this
parameter are 1.4-1.9 Å.
-
probew [float] (1.4) : radius of solvent probe used to
calculate the accessibilities of solute 2's atoms. A
recommended value to use is 1.4 Å. This value is
especially important if the hydrophobic desolvation
term is used, because the calculated accessibilities
are used to calculate the hydrophobic desolvation
energy and forces.
-
threshold [float] (0.) : accessibility threshold - only the
atoms of solutes with accessibility larger than
threshold (Å) are designated as
surface atoms. Moreover, only these atoms are used in
calculating hydrophobic interactions and soft-core
repulsion (repulsive Lennard-Jones). The default value
is 0. for sda_2proteins and, 5. for sdamm.
-
hexcl [float] (0.5) : spacing of the exclusion grid with
which a solute is represented. Does not apply to SDAMM
calculations where the exclusion grid is replaced by a
soft-core repulsion. hexcl defines the
accuracy with which the shape of the solute is
described. Typical values are 0.5-1.0 Å for all-atom
models of proteins. It needs to be consistent
with the timestep used for BD moves - the spatial
accuracy of the protein representation should be
comparable to an average BD move in realistic
simulations.
-
Saving data computed during the initialisation phase
The files will be saved in the directory where the
pdb files are deposited.
save_exclusion [integer,0,1,2] (0) : if > 0, tries to read (and write)
the exclusion grid from/into the disk. The grid can be
loaded in VMD.
-
0
: force recomputation
of the exclusion grid during the
initialisation
-
1
: save the grid in
binary format
-
2
: save the grid in
ascii format
save_access [logical] (0) : if 1, tries to read (and write) the
list of accessible atoms from/to disk. It may save a
lot of time if there are more than 100 000 atoms
present in a pdb file
-
0
: force recomputation
of the accessible atoms during the
initialisation
-
1
: save the data in
ascii format
Multiplicative factors applied to the grids
-
epfct [float] (0.5) : factor by which the electrostatic
potential grid values read in are to be multiplied.
Should be 0.5 if no modifications are
needed.(Equivalent to setting 1.0 in previous verisons
of SDA)
-
edfct [float] (1.67) : factor by which the electrostatic
desolvation potential grid values are to be multiplied.
The value 1.00 corresponds to the uncorrected
electrostatic desolvation penalty for a charge in a
solvent due to the low dielectric cavity of a solute
treated as a collection of van der Waals spheres. More
appropriate factors can be derived by comparing SDA
calculated energies of recorded complexes with energies
calculated with more accurate methods (solving the
finite difference Poisson-Boltzmann equation, for
example). Recommended value:1.67 (with solute interior
dielectric constant set to 4 and the dielectric
boundary between the solute interior and high
dielectric solvent defined by the van der Waals surface
of the solute).
(Gabdoulline, R. R.; Wade, R. C., J. Mol. Biol. 1999,
291, 149-162)
-
hdfct [float] (-0.013) : factor by which the hydrophobic
desolvation potential grid values are to be multiplied.
In the SDA program, hydrophobic desolvation energies
are calculated by multiplying the solvent
accessibilities of the atoms of one of the solutes by
the value of the hydrophobic desolvation potential grid
calculated for the other solute. If the grid is
calculated so that the sum of contributions from all
accessible atoms gives the buried solvent accessible
area, then realistic values for this factor are in the
range -0.0050 to -0.060 kcal/mole/Å2
(or -5 to -60 cal/mole/Å2). The value
of this factor can also be derived by comparing SDA
calculated energies of recorded complexes with energies
calculated with more accurate methods. E.g. values of
-0.013 to -0.019 kcal/mole/Å2 were used in
Gabdoulline R.R., Wade. R.C. JACS, 2009, 131, 9230.
Article
link
-
ljfct [float] ( 1.0) : factor by which the Lennard-Jones
potential grid values are to be multiplied.
-
lj_ref_fct [float] ( 1.0) : factor by which the soft-core
repulsion (repulsive Lennard-Jones) grid are
multiplied. It is used only with sdamm, and replaces
the exclusion grid.
-
Other parameters
-
restart [string] ( empty ) : input file from which the initial
solute positions are read (sda_energy, sda_koff,
sdamm). If this is commented, the positions in the
input pdb files will be used as the starting positions
instead (for sda_koff)
-
account_occurency [bool] ( 0 ) : Only in the case of
sda_koff, if set to 1, the trajectory
will restart n_occurency * nrun times
with the initial position given by the complex.
-
novers [integer] ( 150 ) : number of overlaps allowed before
making a boost. Recommended value: 100-200. With a
value in this range, boosts are usually not necessary
unless the interactions are very strong. This can be
the case if a very small probe size
(probep) is chosen. Many boosts
indicate erroneous input.
-
rboost [float]( 1.0 ) : boost distance (in Å) to move the
solutes apart when more than novers
moves were not accepted due to overlaps. Boosting
is introduced to avoid infinite trajectories and can
influence simulation results because trajectories are
modified by boosts. The number of boosts is reported in
the output log.
-
Parameters specific to the ProMetCS force field
-
correction_image_charge
[float]( 0.0 ) : a non-zero positive number means that
the analytical correction will be applied in computing
the image charge electrostatics. This parameter is also
used to re-scale effective charges when image-charge
electrostatics is computed analytically (at small
distances from the surface when the solute-surface
interface is partially desolvated).
If the protein effective charges do not deviate
strongly from the test charges in magnitude (this is
usually the case for proteins), use
correction_image_charge = 1.
However, if the effective charges of a solute are too
small (as for the case of DNA simulation), the
parameter correction_image_charge enables correcting
back (particularly, to increase) solute charges to test
charges when they are used for the calculation of
image-charge electrostatics at small solute-surface
distances
Note, that the parameter image_charge
= 1 must be defined to use this function.
-
If correction_image_charge > 0, the dielectric
constant for the case of atomic cavities in the
solute molecule close to the surface is scaled as
follows:
ε=4.0+A*z*z+exp(-z/B - C) for 2.5 < z < 5.5 Å,
where :
- A ; default value: A = 0.8 1/Ų
- B ; default value: B = 0.39 1/Å
- C ; default value: C = 10.4
These parameters have been derived from MD
simulations to compute the total electrostatic
interaction energy for a test charge atom as a
function of the distance from a gold surface and are
hard-coded in the file mod_compute_image_charge.f90
(ep_scaleA, ep_scaleB and ep_scaleC)
-
desolv_image_charge
[integer](
0 ) : indicates if
the image charge calculation includes the electrostatic
desolvation term.
If it is equal to 0, it is desactivated but will be
automatically switched on if the electrostatic image
charge is computed.
To force the desactivation of this term in this case,
use desolv_image_charge = -1.
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