add a b
UNIT/RESIDUE/ATOM _a_
UNIT/RESIDUE/ATOM _b_
Add the object _b_ to the object _a_. This command is used to place
ATOMs within RESIDUEs, and RESIDUEs within UNITs.
addAtomTypes {
{ "H" "H" "sp3" }
{ "HO" "H" "sp3" }
...
}
Add mapping of AMBER atom type to element and hybridization. Typically in
leaprc.
addH obj
UNIT _obj_
Add missing hydrogens and build external coordinates for _obj_.
addIons unit ion1 #ion1 [ion2 #ion2]
UNIT _unit_
UNIT _ion1_
NUMBER _#ion1_
UNIT _ion2_
NUMBER _#ion2_
Adds counterions in a shell around _unit_ using a Coulombic potential
on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be
opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise,
the specified numbers of _ion1_ [_ion2_] are added [in alternating order].
If solvent is present, it is ignored in the charge and steric calculations,
and if an ion has a steric conflict with a solvent molecule, the ion is
moved to the center of said molecule, and the latter is deleted. (To
avoid this behavior, either solvate _after_ addIons, or use addIons2.)
Ions must be monoatomic. Note that the one-at-a-time procedure is not
guaranteed to globally minimize the electrostatic energy. When neutralizing
regular-backbone nucleic acids, the first cations will generally be added
between phosphates, leaving the final two ions to be placed somewhere around
the middle of the molecule.
The default grid resolution is 1 Angstrom, extending from an inner radius
of (max ion size + max solute atom size) to an outer radius 4 Angstroms
beyond. A distance-dependent dielectric is used for speed.
addIons2 unit ion1 #ion1 [ion2 #ion2]
UNIT _unit_
UNIT _ion1_
NUMBER _#ion1_
UNIT _ion2_
NUMBER _#ion2_
Same as addIons, except solvent and solute are treated the same.
addIonsRand unit ion1 #ion1 [ion2 #ion2] [separation]
UNIT _unit_
UNIT _ion1_
NUMBER _#ion1_
UNIT _ion2_
NUMBER _#ion2_
NUMBER _separation_
Adds counterions in a shell around _unit_ by replacing random solvent
molecules. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be
opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise,
the specified numbers of _ion1_ [_ion2_] are added [in alternating order].
If _separation_ is specified, ions will be guaranteed to be more than that
distance apart in Angstroms.
Ions must be monoatomic. This procedure is much faster than addIons, as
it does not calculate charges. Solvent must be present. It must be possible
to position the requested number of ions with the given separation in the
solvent.
addPath path
STRING _path_
Add the directory in _path_ to the list of directories that are searched
for files specified by other commands.
addPdbAtomMap list
LIST _list_
The atom Name Map is used to try to map atom names read from PDB files
to atoms within residue UNITs when the atom name in the PDB file does
not match an atom in the residue. This enables PDB files to be read
in without extensive editing of atom names. The LIST is a LIST of LISTs:
{ {sublist} {sublist} ... }
where each sublist is of the form
{ "OddAtomName" "LibAtomName" }
Many `odd' atom names can map to one `standard' atom name, but any single
odd atom name maps only to the last standard atom name it was mapped to.
addPdbResMap list
LIST _list_
The Name Map is used to map residue names read from PDB files to variable
names within LEaP. The LIST is a LIST of LISTs:
{ {sublist} {sublist} ... }
Each sublist contains two or three entries to add to the Name Map:
{ [terminalflag] PDBName LEaPVar }
where the PDBName will be mapped to the LEaPVar. The terminalflag indicates
the special cases of terminal residues: allowable values are 0 for beginning
residues (N-terminal for proteins, 5' for nucleic acids) and 1 for ending
residues (C-terminal for proteins, 3' for nucleic acids). If the
terminalflag is given, the PDBName->LEaPVar name map will only be applied
for the appropriate terminal residue. The `leaprc' file included with
the distribution contains default mappings.
alias [alias[ string]]
STRING _alias_
STRING _string_
alias string1 command - equivalence string1 to command.
alias string1 - delete the alias for string1.
alias - report all current aliases.
alignAxes unit
UNIT _unit_
Translate the geometric center of _unit_ to the origin and align
the principle axes of the ATOMs within _unit_ along the coordinate
axes. This is done by calculating the moment of inertia of the UNIT
using unit mass for each ATOM, and then diagonalizing the resulting
matrix and aligning the eigenvectors along the coordinate axes.
This command modifies the coordinates of the UNIT. It may be
especially useful for preparing long solutes such as nucleic acids
for solvation.
bond atom1 atom2 [ order ]
ATOM _atom1_
ATOM _atom2_
STRING _order_
Create a bond between _atom1_ and _atom2_. Both of these ATOMs must
be contained by the same UNIT. By default, the bond will be a single
bond. By specifying "S", "D", "T", or "A" as the optional argument
_order_ the user can specify a single, double, triple, or aromatic
bond.
bondByDistance container [ maxBond ]
UNIT/RESIDUE/ATOM _container_
NUMBER _maxBond_
Create single bonds between all ATOMs in _container_ that are within
_maxBond_ angstroms of each other. If _maxBond_ is not specified,
a default distance of 2 angstroms used.
center container
UNIT/RESIDUE/ATOM _container_
Display the coordinates of the geometric center of the ATOMs within
_container_.
charge container
UNIT/RESIDUE/ATOM _container_
This command calculates the total charge of the ATOMs within _container_.
The unperturbed and perturbed total charge are displayed.
check unit [ parmset ]
UNIT _unit_
PARMSET/STRING _parmset_
This command can be used to check the UNIT for internal inconsistencies
that could cause problems when performing calculations. This is
a very useful command that should be used before a UNIT is saved
with saveAmberParm or its variations.
With the optional parmset, all missing parameters are placed in the
PARMSET to allow for easy editing of those parameters. If a string is
passed, a PARMSET will be created with that name.
Currently it checks for the following possible problems:
- Long bonds. A long bond is greater than 3.0 angstroms.
- Short bonds. A short bond is less than 0.5 angstroms.
- Non-integral total charge of the UNIT.
- Missing types.
- Close contacts between non-bonded ATOMs. A close contact is
less than 1.5 angstroms.
clearPdbAtomMap
Clear the Name Map used for ``second-chance'' mapping of atom names in
PDB files to atoms within residue UNITs. See addPdbAtomMap.
clearPdbResMap
Clear the Name Map used to map residue names in PDB files to variable
names within LEaP. See addPdbResMap.
clearVariables [ list ]
LIST _list_
This command removes variables from LEaP. If the _list_ argument
is provided, then only the variables in the LIST will be removed.
If no argument is provided then ALL variables will be removed.
variable = combine list
object _variable_
LIST _list_
Combine the contents of the UNITs within _list_ into a single UNIT.
The new UNIT is placed in _variable_. This command is similar to
the sequence command except it does not link the ATOMs of the UNITs
together.
newvariable = copy variable
object _newvariable_
object _variable_
Create an exact duplicate of the object _variable_. Changing the object
_variable_ will not affect the object _newvariable_.
This is in contrast to the situation created by "newvariable = variable"
in which both names reference the same object.
variable = createAtom name type charge
ATOM _variable_
STRING _name_
STRING _type_
NUMBER _charge_
Return a new ATOM with _name_, _type_, and _charge_.
variable = createParmset name
PARMSET _variable_
STRING _name_
Return a new and empty PARMSET with the name _name_.
variable = createResidue name
RESIDUE _variable_
STRING _name_
Return a new and empty RESIDUE with the name _name_.
variable = createUnit name
UNIT _variable_
STRING _name_
Return a new and empty UNIT with the name _name_.
crossLink res1 conn1 res2 conn2
RESIDUE _res1_
STRING _connect1_
RESIDUE _res2_
STRING _connect2_
Create a bond between ATOMs at the connection point specified by
_conn1_ and _conn2_. The argument _conn1_ and _conn2_ can have the
following values:
Name_ Alternatives__
$connect0 $nend, $firstend
$connect1 $cend, $lastend
$connect2 $send, $disulphide
$connect3
$connect4
$connect5
debugOff filename
STRING _filename_
This command is a system debugging function. It turns off debugging
messages from the source (.c) file _filename_. The symbol *
matches all files. The default for all filenames is `off'.
Note that system debugging is in effect only if LEaP was compiled
with the preprocessor macro DEBUG defined.
debugOn filename
STRING _filename_
This command is a system debugging function. It turns on debugging
messages from the source (.c) file _filename_. The symbol *
matches all files. The default for all filenames is `off'.
Note that system debugging is in effect only if LEaP was compiled
with the preprocessor macro DEBUG defined.
debugStatus
This command is a memory debugging function. It displays various
messages that describe LEaP's usage of system resources.
Note that memory debugging is in effect only if LEaP was compiled
with the preprocessor macro MEMORY_DEBUG defined; MEMORY_DEBUG values
range from 1 through 4 with the greatest being the most aggressive.
deleteBond atom1 atom2
ATOM _atom1_
ATOM _atom2_
Remove the bond between the ATOMs _atom1_ and _atom2_. If no bond
exists, an error will be displayed.
deleteOffLibEntry library entry
STRING _library_
STRING _entry_
Delete _entry_ from the Object File Format file named _library_.
deleteRestraint unit a b [c [d]]
UNIT _unit_
ATOM _a_
ATOM _b_
ATOM _c_
ATOM _d_
Remove a bond, angle, or torsion restraint from _unit_, depending
on the number of ATOMs specified.
desc variable
object _variable_
Print a description of the object.
deSelect obj
UNIT/RESIDUE/ATOM _obj_
Clears the SELECT flag on all ATOMs within _obj_. See the select command.
displayPdbAtomMap
Display the Name Map used for ``second chance'' mapping of atom names
in PDB files to atoms within residue UNITs. See addPdbAtomMap.
displayPdbResMap
Display the Name Map used to map residue names in PDB files to variable
names within LEaP. See addPdbResMap.
edit unit-parmset
UNIT/PARMSET _unit-parmset_
In xLEaP this command creates a unit editor or parameter set editor
that contains the UNIT or PARMSET _unit-parmset_. The user can view
and edit the contents of the UNIT or PARMSET by using the mouse.
If _unit-parmset_ is a PARMSET, then the user may select the Atom, Bond,
Angle, Torsion, Improper Torsion, or Hydrogen Bond Parameters to
edit by selecting the appropriate button.
In tLEaP this command prints an error message.
flip obj
UNIT _obj_
Flips the chirality of the selected atoms within _obj_.
groupSelectedAtoms unit name
UNIT _unit_
STRING _name_
Create a group within _unit_ with the name _name_ using all of the
ATOMs within the UNIT that are selected. If the group has already
been defined then overwrite the old group.
help [string]
STRING _string_
This command prints a description of the command in _string_. If
the STRING is not given then a list of legal STRINGs is provided.
impose unit seqlist internals
UNIT _unit_
LIST _seqlist_
LIST _internals_
The impose command allows the user to impose internal coordinates
on the UNIT. The list of RESIDUEs to impose the internal coordinates
upon is in _seqlist_. The internal coordinates to impose are in
the LIST _internals_.
The command works by looking into each RESIDUE within the UNIT that
is listed in the _seqlist_ argument and attempts to apply each of
the internal coordinates within _internals_. The _seqlist_ argument
is a LIST of NUMBERs that represent sequence numbers or ranges of
sequence numbers. Ranges of sequence numbers are represented by
two-element LISTs that contain the first and last sequence number
in the range. The user can specify sequence number ranges that are
larger than what is found in the UNIT. For example the range { 1 999 }
represents all RESIDUEs in a 200 RESIDUE UNIT.
The _internals_ argument is a LIST of LISTs. Each sublist contains
a sequence of ATOM names which are of type STRING followed by the
value of the internal coordinate. See the output of help _types_ for
details on specifying STRINGs. Examples of the impose command are:
impose peptide { 1 2 3 } { { $N $CA $C $N -40.0 } { $C $N $CA $C
-60.0 } }
The RESIDUEs with sequence numbers 1, 2, and 5 within the UNIT peptide
will assume an alpha helix conformation.
impose peptide { 1 2 { 5 10 } 12 } { { "CA" "CB" 5.0 } }
This will impose on the residues with sequence numbers 1, 2, 5, 6,
7, 8, 9, 10, and 12 within the UNIT peptide a bond length of 5.0
angstroms between the alpha and beta carbons. RESIDUEs without an
ATOM named $CB (like glycine) will be unaffected.
Three types of conformational change are supported; bond length changes,
bond angle changes, and torsion angle changes. If the conformational
change involves a torsion angle, then all dihedrals around the central
pair of atoms are rotated. The entire list of internals are applied
to each RESIDUE.
list
List all of the variables currently defined.
listOff library
STRING _library_
List the UNITs/PARMSETs stored within the Object File Format file
named _library_.
variable = loadAmberParams filename
PARMSET _variable_
STRING _filename_
Load an AMBER format parameter set file and place it in _variable_.
All interactions defined in the parameter set will be contained within
_variable_. This command causes the loaded parameter set to be included
in LEaP's list of parameter sets that are searched when parameters are
required. General proper and improper torsion parameters are modified,
the AMBER general type "X" is replaced with the LEaP general type "?".
loadAmberPrep filename [ prefix ]
STRING _filename_
STRING _prefix_
This command loads an AMBER PREP input file. For each residue that
is loaded, a new UNIT is constructed that contains a single RESIDUE
and a variable is created with the same name as the name of the residue
within the PREP file. If the optional argument _prefix_ is provided
it will be prefixed to each variable name; this feature is used to
prefix united atom residues, which have the same names as all-atom
residues, with the string $U to distinguish them.
variable = loadMol2 filename
STRING _filename_
Load a Sybyl Mol2-format file with the file name _filename_. The UNIT
loaded will have the name specified for the MOLECULE in the input file.
variable = loadMol3 filename
STRING _filename_
Load a Sybyl-derived Mol3-format file with the file name _filename_.
The UNIT loaded will have the name specified for the MOLECULE in the
input file.
More information:
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
loadOff filename
STRING _filename_
This command loads the Object File Format library within the file named
_filename_. All UNITs and PARMSETs within the library will be loaded.
The objects are loaded into LEaP under the variable names the objects
had when they were saved. Variables already in existence that have the
same names as the objects being loaded will be overwritten. PARMSETs
loaded using this command are included in LEaP's library of PARMSETs
that is searched whenever parameters are required.
variable = loadPdb filename
STRING _filename_
Load a Protein Data Bank format file with the file name _filename_.
The sequence numbers of the RESIDUEs will be determined from the order
of residues within the PDB file ATOM records. For each residue in the
PDB file, LEaP searches the variables currently defined for variable
names that match the residue name. If a match is found then the
contents of the variable are copied into the UNIT created for the PDB
structure. If no PDB `TER' card separates the current residue from the
previous one, a bond is created between the connect1 ATOM of the
previous residue and the connect0 atom of the new one. (A PDB TER
record is also used to detect a new residue in the case of contiguous
residues with identical residue sequence numbers.) As atoms are read
from the ATOM records, their coordinates are written into the
correspondingly named ATOMs within the residue being built. If the
entire residue is read and it is found that ATOM coordinates are missing
then external coordinates are built from the internal coordinates that
were defined in the matching UNIT (residue) variable. This allows LEaP
to build coordinates for hydrogens and lone pairs which are not
specified in PDB files.
loadPdbUsingSeq filename unitlist
STRING _filename_
LIST _unitlist_
This command reads a Protein Data Bank format file from the file
named _filename_. This command is identical to loadPdb except it
does not use the residue names within the PDB file. Instead, the
sequence is defined by the user in _unitlist_. For more details
see loadPdb.
logFile filename
STRING _filename_
This command opens the file with the file name _filename_ as a log
file. User input and ALL output is written to the log file. Output
is written to the log file as if the verbosity level were set to 2.
variable = matchVariables string
LIST _variable_
STRING _string_
Create a LIST of variables with names that match _string_. The _string_
argument can contain the wildcard characters "?" and "*" to match any
single character or substring of characters, respectively.
measureGeom atom1 atom2 [ atom3 [ atom4 ] ]
ATOM _atom1_ _atom2_ _atom3_ _atom4_
Measure the distance, angle, or torsion between two, three, or four ATOMs,
respectively.
quit
relax obj
UNIT _obj_
Relaxes the selected atoms within _obj_.
remove a b
UNIT/RESIDUE/ATOM _a_
UNIT/RESIDUE/ATOM _b_
Remove the object _b_ from the object _a_. If _a_ is not contained
by _b_ then an error message will be displayed. This command is
used to remove ATOMs from RESIDUEs, and RESIDUEs from UNITs. If
the object represented by _b_ is not referenced by some variable
name then it will be destroyed.
restrainAngle unit a b c force angle
UNIT _unit_
ATOM _a_
ATOM _b_
ATOM _c_
NUMBER _force_
NUMBER _angle_
Add an angle restraint to _unit_ between atoms _a_, _b_, and _c_,
having force constant of _force_, and equilibrium angle _angle_.
restrainBond unit a b force length
UNIT _unit_
ATOM _a_
ATOM _b_
NUMBER _force_
NUMBER _length_
Add a bond (distance) restraint to _unit_ between atoms _a_ and _b_
with a force constant of _force_ and an equilibrium distance of _length_.
restrainTorsion unit a b c d force phi multiplicity
UNIT _unit_
ATOM _a_
ATOM _b_
ATOM _c_
ATOM _d_
NUMBER _force_
NUMBER _phi_
NUMBER _multiplicity_
Add a torsion restraint to _unit_ between atoms _a_, _b_, _c_, and
_d_, with a force constant of _force_, an equilibrium torsion angle
of _phi_, and a multiplicity of _multiplicity_.
saveAmberParm unit topologyfilename coordinatefilename
UNIT _unit_
STRING _topologyfilename_
STRING _coordinatefilename_
Save the AMBER topology and coordinate files for the UNIT into the
files named _topologyfilename_ and _coordinatefilename_ respectively.
This command will cause LEaP to search its list of PARMSETs for
parameters defining all of the interactions between the ATOMs within
the UNIT. This command produces a topology file and a coordinate file
which are identical in format to those produced by the AMBER program
PARM, and which can be read into AMBER and SPASMS for energy minimization,
dynamics, or nmode calculations.
See also: saveAmberParmPol, saveAmberParmPert, and saveAmberParmPolPert
for including atomic polarizabilities and preparing free energy
perturbation calculations and saveAmberParmNetcdf for saving in a
binary format.
saveAmberParmNetcdf unit topologyfilename coordinatefilename
UNIT _unit_
STRING _topologyfilename_
STRING _coordinatefilename_
Save the AMBER topology and coordinate files for the UNIT into the
files named _topologyfilename_ and _coordinatefilename_ respectively.
This command will cause LEaP to search its list of PARMSETs for
parameters defining all of the interactions between the ATOMs within
the UNIT. This command produces a topology file and a coordinate file
which can be read into AMBER and SPASMS for energy minimization, dynamics,
or nmode calculations.
The coordinate file written will be in the binary NetCDF AMBER restart
format, which enables the writing of larger input files and quicker I/O.
Use saveAmberParm for the regular ASCII coordinate format.
saveAmberParmPert unit topologyfilename coordinatefilename
UNIT _unit_
STRING _topologyfilename_
STRING _coordinatefilename_
Save the AMBER topology and coordinate files for the UNIT into the
files named _topologyfilename_ and _coordinatefilename_ respectively.
This command will cause LEaP to search its list of PARMSETs for
parameters defining all of the interactions between the ATOMs within
the UNIT - including the perturbed ATOMs (which are ignored by the
vanilla saveAmberParm command). This command produces a topology file
and a coordinate file that are identical in format to those produced by
the AMBER PARM program using the PERT option, and which can be read into
AMBER and SPASMS for free energy calculations.
saveAmberParmPol unit topologyfilename coordinatefilename
Like saveAmberParm, but includes atomic polarizabilities in the topology
file for use with IPOL=1 in Sander. The polarizabilities are according
to atom type, and are defined in the 'mass' section of the parm.dat or
frcmod file. Note: charges are normally scaled when polarizabilities are
used - see scaleCharges for an easy way of doing this.
saveAmberParmPolPert unit topologyfilename coordinatefilename
Like saveAmberParmPert, but includes atomic polarizabilities in the topology
file for use with IPOL=1 in Gibbs. The polarizabilities are according to
atom type, and are defined in the 'mass' section of the parm.dat or frcmod
file. Note: charges are normally scaled when polarizabilities are used -
see scaleCharges for an easy way of doing this.
saveAmberPrep unit filename
UNIT _unit_
STRING _filename_
Save all residues in the UNIT to a prep.in file. All possible improper
dihedrals are given for each residue, so unwanted ones need to be
deleted from the file. 'Connect0' and 'connect1' atoms must be defined
for each residue.
saveMol2 unit filename option
UNIT _unit_
STRING _filename_
NUMBER _option_
Write UNIT to the file _filename_ as a Mol2 format file.
option = 0 for Default atom types
option = 1 for AMBER atom types
More information:
https://upjv.q4md-forcefieldtools.org/Tutorial/leap-mol2.php
saveMol3 unit filename option
UNIT _unit_
STRING _filename_
NUMBER _option_
Write UNIT to the file _filename_ as a Mol3 format file.
option = 0 for Default atom types
option = 1 for AMBER atom types
More information:
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
saveOff object filename
object _object_
STRING _filename_
The saveOff command allows the user to save UNITs, and PARMSETs to a
file named _filename_. The file is written using the Object File
Format (OFF) and can accommodate an unlimited number of uniquely
named objects. The names by which the objects are stored are the
variable names specified in the argument of this command. If the
file _filename_ already exists then the new objects will be added
to the file. If there are objects within the file with the same
names as objects being saved then the old objects will be overwritten.
The argument _object_ can be a single UNIT, a single PARMSET, or
a LIST of mixed UNITs and PARMSETs.
savePdb unit filename
UNIT _unit_
STRING _filename_
Write UNIT to the file _filename_ as a PDB format file.
scaleCharges container scale_factor
UNIT/RESIDUE/ATOM _container_
NUMBER _scale_factor_
This command scales the charges in the object by _scale_factor_,
which must be > 0. It is useful for building systems for use
with polarizable atoms, e.g.
> x = copy solute
> scaleCharges x 0.8
> y = copy WATBOX216
> scalecharges y 0.875
> solvatebox x y 10
> saveamberparmpol x x.top x.crd
select obj
UNIT/RESIDUE/ATOM _obj_
Sets the SELECT flag on all ATOMs within _obj_. See the deSelect command.
variable = sequence list
LIST _list_
The sequence command is used to create a new UNIT by copying the
contents of a LIST of UNITs. As each UNIT in the list is copied,
a bond is created between its head atom and the tail ATOM of the
previous UNIT, if both connect ATOMs are defined. If only one of
the connect pair is defined, a warning is generated and no bond is
created. If neither connection ATOM is defined then no bond is
created. As each RESIDUE within a UNIT is copied, it is assigned a
sequence number reflecting the order added. The order of RESIDUEs
in multi-RESIDUE UNITs is maintained.
This command builds reasonable starting coordinates for the new UNIT
by assigning internal coordinates to the linkages between the component
UNITs and building the Cartesian coordinates from these and the
internal coordinates of the component UNITs.
set default variable value
STRING _variable_
STRING _value_
OR
set container parameter object
UNIT/RESIDUE/ATOM/STRING _container_
STRING _parameter_
object _object/value_
This command sets the values of some global parameters (when the first
argument is "default") or sets various parameters associated with _container_.
To see the possible variables for "set default", type "help set_default".
The box parameter of a UNIT defines the bounding box of the UNIT; this is
not a UNIT's periodic box. The setBox and solvate family of commands add a
periodic box to a UNIT; for a description, type, e.g., "help setBox".
The more useful parameters for each type of _container_ are the following:
container parameters values
UNIT name STRING
head, tail ATOM [e.g. unit.1.1]
restype "protein" "nucleic" "saccharide" "solvent"
"undefined" [sets all residues in UNIT]
box LIST [side lengths: {A B C}]
or NUMBER [cube side length] or "null"
cap LIST [center, radius: {X Y Z R}]
or "null"
RESIDUE name STRING
[e.g. restype [see UNIT]
unit.1] connect0, connect1 ATOM [e.g. unit.1.1]
imagingAtom ATOM [e.g. unit.1.1]
ATOM name, pertName STRING [<= 4 chars]
[e.g. type, pertType STRING [<= 2 chars]
unit.1.1] element STRING
pert "true" [or pert flag unset]
charge, pertCharge DOUBLE
position LIST [{X Y Z}]
Allowed arguments to "set default variable value" are these:
variables values descriptions
PdbWriteCharges "on" add charges to each ATOM record
"off" don't do this (default)
OldPrmtopFormat "on" use prmtop format from Amber6 and earlier
"off" use the new prmtop format (default)
Gibbs "on" require perturbed atoms to be set explicitly
(needed for gibbs)
"off" set perturbed if Type != PertType (default)
(OK for sander)
UseResIds "on" put cols 22-27 of the input pdb file into
"off" a RESIDUE_ID table in prmtop files; default
is "off"; only works with new prmtop formats,
and when a single loadPdb command is used to
create a unit.
Charmm "on" include terms for CHARMM22 force fields
"off" don't include these (default)
DeleteExtraPointAngles
"on" delete angles and torsions relating to
extra points (default)
"off" don't delete these (for older codes only)
FlexibleWater "on" allow for flexible 3-point water models
"off" assume 3-point water models are rigid (default)
PBRadii "bondi" use Bondi radii for generalized Born
"mbondi" use H-modified Bondi radii (default)
"mbondi2" use H(N)-modified Bondi radii
"mbondi3" ArgH and AspGluO modified Bondi2 radii
"parse" Radii from the Sitkoff et al. parse parameters
"pbamber" Huo and Kollman optimized radii (old!)
"amber6" use radii that were the default in amber6
(only recommended for backwards compat.)
Dielectric "distance" use distance-dependent dielectric (default)
"constant" use constant dielectric
dipole_damp_factor real sets the default value for "DIPOLE_DAMP_FACTOR"
for dipole screening factors in Thole models.
Valid value > 0.0
sceescalefactor real sets the default value for "SCEE_SCALE_FACTOR"
for 1-4 EEL scaling factors. Valid value > 0.0.
Default=1.2.
scnbscalefactor real sets the default value for "SCNB_SCALE_FACTOR"
for 1-4 NB scaling factors. Valid value > 0.0.
Default=2.0.
CMAP "on" include CMAP corrections for dihedrals
"off" don't include these (default)
PHIPSIMAP "on" include residue-based PHIPSI parameters
"off" don't include these (default)
ipol integer Sets the default value for IPOL.
Valid values are 0 - 4.
Default value is 0, meaning disabled.
nocenter "on" coordinates will not be centered in the
periodic simulation box
"off" coordinates will be centered (default)
reorder_residues "on" solvent will be moved to the end (default)
"off" residue order will be maintained as input.
Beta feature: use at your own risk!
setBox solute enclosure [ buffer ]
UNIT _solute_
"vdw" OR "centers" _enclosure_
object _buffer_
The setBox command creates a periodic box around the _solute_ UNIT, turning
it into a periodic system for the simulation programs. It does not add
any solvent to the system. The choice of "vdw" or "centers" determines
whether the box encloses all entire atoms or just all atom centers -
use "centers" if the system has been previously equilibrated as a
periodic box. See the solvateBox command for a description of the
buffer object, which extends either type of box by an arbitrary amount.
showDefault [ variable OR all OR * ]
STRING _variable_
The showdefault command shows the values assigned to the variables by
the "set default" command. Without variable, with "all", or with "*",
all default variables are shown.
solvateBox solute solvent buffer [ "iso" ] [ closeness ]
UNIT _solute_
UNIT _solvent_
object _buffer_
NUMBER _closeness_
The solvateBox command creates a solvent box around the _solute_ UNIT.
The _solute_ UNIT is modified by the addition of _solvent_ RESIDUEs.
The user may want to first align long solutes that are not expected
to tumble using alignAxes, in order to minimize box volume.
The normal choice for a TIP3 _solvent_ UNIT is WATBOX216. Note that
constant pressure equilibration is required to bring the artificial box
to reasonable density, since Van der Waals voids remain due to the
impossibility of natural packing of solvent around the solute and at
the edges of the box.
The solvent box UNIT is copied and repeated in all three spatial directions
to create a box containing the entire solute and a buffer zone defined
by the _buffer_ argument. The _buffer_ argument defines the distance,
in angstroms, between the wall of the box and the closest ATOM in the
solute.
If the buffer argument is a single NUMBER, then the buffer distance is
the same for the x, y, and z directions, unless the "iso" option is used
to make the box isometric, with the shortest box clearance = buffer. If
"iso" is used, the solute is rotated to orient the principal axes,
otherwise it is just centered on the origin.
If the buffer argument is a LIST of three NUMBERS, then the NUMBERs are
applied to the x, y, and z axes respectively. As the larger box is created
and superimposed on the solute, solvent molecules overlapping the solute
are removed.
The optional _closeness_ parameter can be used to control the extent to
which _solvent_ ATOMs overlap _solute_ ATOMs. The default value of
the _closeness_ argument is 1.0, which allows no overlap. Smaller
values allow solvent ATOMs to overlap _solute_ ATOMs by (1 - closeness) *
R*ij, where R*ij is the sum of the Van der Waals radii of solute and
solvent atoms. Values greater than 1 enforce a minimum gap between
solvent and solute of (closeness - 1) * R*ij.
This command modifies the _solute_ UNIT in several ways. First, the
coordinates of the ATOMs are modified to move the center of a box
enclosing the Van der Waals radii of the atoms to the origin. Secondly,
the UNIT is modified by the addition of _solvent_ RESIDUEs copied from
the _solvent_ UNIT. Finally, the box parameter of the new system (still
named for the _solute_) is modified to reflect the fact that a periodic,
rectilinear solvent box has been created around it.
solvateCap solute solvent position radius [ closeness ]
UNIT _solute_
UNIT _solvent_
object _position_
NUMBER _radius_
NUMBER _closeness_
The solvateCap command creates a solvent cap around the _solute_ UNIT
or a part thereof. The _solute_ UNIT is modified by the addition of
_solvent_ RESIDUEs.
The normal choice for a TIP3 _solvent_ UNIT is WATBOX216. The _solvent_
box is repeated in all three spatial directions and _solvent_ RESIDUEs
selected to create a solvent sphere with a radius of _radius_ Angstroms.
The _position_ argument defines where the center of the solvent cap
is to be placed. If _position_ is a UNIT, RESIDUE, ATOM, or a LIST
of UNITs, RESIDUEs, or ATOMs, then the geometric center of the ATOMs
within the object will be used as the center of the solvent cap sphere.
If _position_ is a LIST containing three NUMBERs then the _position_
argument will be treated as a vector that defines the position of
the solvent cap sphere center.
The optional _closeness_ parameter can be used to control the extent to
which _solvent_ ATOMs overlap _solute_ ATOMs. The default value of
the _closeness_ argument is 1.0, which allows no overlap. Smaller
values allow solvent ATOMs to overlap _solute_ ATOMs by (1 - closeness) *
R*ij, where R*ij is the sum of the Van der Waals radii of solute and
solvent atoms. Values greater than 1 enforce a minimum gap between
solvent and solute of (closeness - 1) * R*ij.
This command modifies the _solute_ UNIT in several ways. First,
the UNIT is modified by the addition of _solvent_ RESIDUEs copied
from the _solvent_ UNIT. Secondly, the cap parameter of the UNIT
_solute_ is modified to reflect the fact that a solvent cap has been
created around the solute.
solvateDontClip solute solvent buffer [ closeness ]
UNIT _solute_
UNIT _solvent_
object _buffer_
NUMBER _closeness_
This command is identical to the solvateBox command except that the
solvent box that is created is not clipped to the boundary of the
_buffer_ region. This command forms larger solvent boxes than does
solvateBox because it does not cause solvent that is outside the buffer
region to be discarded. This helps to preserve the periodic structure
of properly constructed solvent boxes, preventing hot-spots from
forming.
solvateOct solute solvent buffer [ "iso" ] [ closeness ]
UNIT _solute_
UNIT _solvent_
object _buffer_
NUMBER _closeness_
The solvateOct command is the same as solvateBox, except the corners
of the box are sliced off, resulting in a truncated octahedron, which
typically gives a more uniform distribution of solvent around the
solute.
In solvateOct, when a LIST is given for the buffer argument, four
numbers are given instead of three, where the fourth is the diagonal
clearance. If 0.0 is given as the fourth number, the diagonal clearance
resulting from the application of the x,y,z clearances is reported. If
a non-0 value is given, this may require scaling up the other clearances,
which is also reported. Similarly, if a single number is given, any
scaleup of the x,y,z buffer to accommodate the diagonal clip is reported.
If the "iso" option is used, the isometric truncated octahedron is
rotated to an orientation used by the PME code, and the box and angle
dimensions output by the saveAmberParm* commands are adjusted for PME
code imaging.
solvateShell solute solvent thickness [ closeness ]
UNIT _solute_
UNIT _solvent_
NUMBER _thickness_
NUMBER _closeness_
The solvateShell command creates a solvent shell around the _solute_ UNIT.
The _solute_ UNIT is modified by the addition of _solvent_ RESIDUEs.
The normal choice for a TIP3 _solvent_ UNIT is WATBOX216. The _solvent_ box
is repeated in all three spatial directions and _solvent_ RESIDUEs selected
to create a solvent shell with a radius of _thickness_ Angstroms around the
_solute_.
The _thickness_ argument defines the maximum distance a _solvent_ ATOM may
be from the closest _solute_ ATOM.
The optional _closeness_ parameter can be used to control overlap of _solvent_
with _solute_ ATOMs. The default value of the _closeness_ argument is
1.0, which allows contact but no overlap. Please see the solvateBox
command for more details on the _closeness_ parameter.
source filename
STRING _filename_
This command executes LEaP commands within a text file. To display the
commands as they are read, see the verbosity command. The text within
the source file must be formatted exactly like the text the user types
into LEaP.
transform atoms matrix
CONTAINER/LIST _atoms_
LIST _matrix_
Translate all of the ATOMs within _atoms_ by the (3X3) or (4X4) matrix
defined by the 9 or 16 NUMBERs in the LIST of LISTs _matrix_.
{ { r11 r12 r13 -tx }
{ r21 r22 r23 -ty }
{ r31 r32 r33 -tz }
{ 0 0 0 1 } }
The diagonal upper left elements, rII can be used for symmetry operations,
e.g. a reflection in the XY plane can be produced with r11=1, r22=1, r33=-1
where the other rIJ elements are 0. The -t column is used to specify
translations along the appropriate axes (0 for no translation).
translate atoms direction
UNIT/RESIDUE/ATOM _atoms_
LIST _direction_
Translate all of the ATOMs within _atoms_ by the vector defined by
the three NUMBERs in the LIST _ direction_.
verbosity level
NUMBER _level_
This command sets the level of output that LEaP provides the user.
A value of 0 is the default, providing the minimum of messages. A
value of 1 will produce more output, and a value of 2 will produce
all of the output of level 1 and display the text of the script lines
executed with the source command.
zMatrix obj zmatrix
UNIT/RESIDUE/ATOM _obj_
LIST _zmatrix_
The zMatrix command is quite complicated. It is used to define the
external coordinates of ATOMs within _obj_ using internal coordinates.
The second parameter of the zMatrix command is a LIST of LISTs; each
sub-list has several arguments:
{ a1 a2 bond12 }
This entry defines the coordinate of _a1_ by placing it _bond12_ angstroms
along the x-axis from ATOM _a2_. If ATOM _a2_ does not have coordinates
defined then ATOM _a2_ is placed at the origin.
{ a1 a2 a3 bond12 angle123 }
This entry defines the coordinate of _a1_ by placing it _bond12_ angstroms
away from ATOM _a2_ making an angle of _angle123_ degrees between
_a1_, _a2_ and _a3_. The angle is measured in a right hand sense
and in the x-y plane. ATOMs _a2_ and _a3_ must have coordinates defined.
{ a1 a2 a3 a4 bond12 angle123 torsion1234 }
This entry defines the coordinate of _a1_ by placing it _bond12_ angstroms
away from ATOM _a2_, creating an angle of _angle123_ degrees between
_a1_, _a2_, and _a3_, and making a torsion angle of _torsion1234_ between
_a1_, _a2_, _a3_, and _a4_.
{ a1 a2 a3 a4 bond12 angle123 angle124 orientation }
This entry defines the coordinate of _a1_ by placing it _bond12_ angstroms
away from ATOM _a2_, making angles _angle123_ between ATOMs _a1_,
_a2_, and _a3_, and _angle124_ between ATOMs _a1_, _a2_, and _a4_. The
argument _orientation_ defines whether the ATOM _a1_ is above or below
a plane defined by the ATOMs _a2_, _a3_, and _a4_. If _orientation_
is positive then _a1_ will be placed in such a way so that the inner
product of (_a3_-_a2_) cross (_a4_-_a2_) with (_a1_-_a2_) is positive.
Otherwise _a1_ will be placed on the other side of the plane. This
allows the coordinates of a molecule like fluoro-chloro-bromo-methane
to be defined without having to resort to dummy atoms.
The first arguments within the zMatrix entries ( _a1_, _a2_, _a3_,
_a4_ ) are either ATOMs or STRINGs containing names of ATOMs within
_obj_. The subsequent arguments are all NUMBERs. Any ATOM can be
placed at the _a1_ position, even those that have coordinates defined.
This feature can be used to provide an endless supply of dummy atoms,
if they are required. A predefined dummy atom with the name "*"
(a single asterisk, no quotes) can also be used.
No order is imposed in the sub-lists. The user can place sub-lists
in arbitrary order, as long as they maintain the requirement that
all atoms _a2_, _a3_, and _a4_ must have external coordinates defined,
except for entries that define the coordinate of an ATOM using only
a bond length.