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
(in degrees), and a periodicity of multiplicity
(see the restrainBond command for an example of this
command).
The following is a description of the commands that can be accessed using the command line interface in tLEAP, or through the command line editor in xLEAP. Whenever an argument in a command line definition is enclosed in brackets ([arg]), then that argument is optional. When examples are shown, the command line is prefaced by "> ", and the program output is shown without this character preface.
add a b
add command
and the way the tip3p water molecule
is created for the LEAP distribution tape.
addAtomTypes { { type element hybrid } { ... } ... }
leaprc
files. The STRINGs are most safely rendered using
quotation marks. If atom types are not defined,
confusing messages about hybridization can result
when loading PDB files.
addIons unit ion1 numIon1 [ion2 numIon2]
addIons unit ion1 numIon1 [ion2 numIon2]
addPath path
After the above command is entered, the program will search for a file in this directory if a file is specified in a command. Thus, if a user has a library named "/disk/howard/rings.lib" and the user wants to load that library, one only needs to enter load rings.lib and not load /disk/howard/rings.lib.
addPdbAtomMap list
where the first string is the name within the PDB file, and the second string is the name in the residue UNIT.
addPdbResMap list
where double can be 0 or 1, the first string is the name within the PDB file, and the second string is the variable name to which the first string will be mapped. To illustrate, the following is part of the Name Map that exists when LEAP is started from the "leaprc" file included in the distribution tape:
Thus, the residue ALA will be mapped to
NALA if it is the N-terminal residue
and CALA if it is found at the C-terminus.
The above Name Map was produced using the following
(edited) command line:
alias [ string1 [ string2 ] ]
The proposed alias is first checked for conflict with the LEAP commands and it is rejected if a conflict is found. A proposed alias will replace an existing alias with a warning being issued. The alias can stand for more than a single word, but also as an entire string so the user can quickly repeat entire lines of input.
The leaprc file that is found in the LEAP distribution tape creates the following aliases:
The following line is an example of this command:
alignAxes unit
The following example illustrates the alignAxes command. For the purposes of this manual, the CA ATOM of the all_amino94.lib UNIT GLY is described. The user should note the change in the CA Cartesian coordinates after alignment.
bond atom1 atom2 [ order ]
bondByDistance container [ maxBond ]
center container
charge container
check unit [ parms ]
The user may collect any missing molecular mechanics parameters in a PARMSET for subsequent editing. In the following example, the alanine UNIT found in the amino acid library has been examined by the check command:
addPdbAtomMap command).
addPdbResMap command).
clearVariables [ list ]
variable = combine list
newvariable = copy variable
In the above example, tripeptide is a separate object from tripeptideSol and is not solvated. Had the user instead entered
then both tripeptide and tripeptideSol would be solvated since they would both point to the same object.
variable = createAtom name type charge
variable = createParmset name
variable = createResidue name
variable = createUnit name
crossLink res1 conn1 res2 conn2 [ order ]
Example:
debugOff filename
debugOn filename
debugStatus [memory]
Command example:
deleteBond atom1 atom2
deleteOffLibEntry library entry
deleteRestraint unit a b [ c [ d ] ]
desc variable
Now, the desc command is used to examine the first residue (1) of the alanine UNIT:
Next, we illustrate the desc command by examining the ATOM n of the first residue (1) of the alanine UNIT:
Since the n ATOM is also the first atom of the ALA residue, the following command will give the same output as the previous example:
deSelect object
edit unit
groupSelectedAtoms unit name
An expression like "TRP@sideChain" returns a LIST, so any commands that require LIST 's can take advantage of this notation. After assignment, one can access groups using the "@" notation. Examples:
The latter example will calculate the center of the atoms in the "sideChain" group. (see the select command for a more detailed example.)
help [string]
impose unit seqlist 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. An example of the impose command would be:
This would cause the RESIDUE with sequence numbers 1, 2, and 3 within the UNIT peptide to assume an alpha helical conformation. The command
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.
listOff library
variable = loadAmberParams filename
The LEAP distribution contains "old" and "new" AMBER force field parameters in files "parm91X.dat" and "parm94.dat". One could build OFF libraries using the commands shown below; at some point this may become a standard conversion, but since it is easier to maintain the parameters in the AMBER format, this procedure is not used in the default setup. "parm91X.dat" is used instead of the "parm91.dat" in the AMBER dat/ tree because this file has corrections for LEAP 's method of applying improper torsions.
loadAmberPrep filename [ prefix ]
CHARGE
0.2442 -0.0207 -0.0207 -0.4057 0.2442
-0.0207 -0.0207
DONE
STOP
This fragment can be loaded into LEAP using the following command:
loadOff filename
variable = loadPdb filename
The above edited listing shows the use of this command to load a PDB file for the protein Crambin. Several disulphide bonds are present in the protein and these bonds are indicated in the PDB file. The loadPdb command, however, cannot read this information from the PDB file. It is necessary for the user to explicitly define disulphide bonds using the crossLink command.
loadPdbUsingSeq filename unitlist
In the above example, a variable is first defined as a LIST of united atom RESIDUEs. A PDB file is then loaded, in this sequence order, from the file "pept.pdb".
logFile filename
variable = matchVariables string
measureGeom atom1 atom2 [ atom3 [ atom4 ] ]
In the following example, we first describe the RESIDUE ALA of the ALA UNIT in order to find the identity of the ATOMs. Next, the measureGeom command is used to determine a distance, simple angle, and a dihedral angle. As shown in the example, the ATOMs may be identified using atom names or numbers.
remove a b
restrainAngle unit a b c force angle
restrainBond unit a b force length
In the above example, we illustrate several commands for adding and removing restraints to the "lib/all_amino94.lib" UNIT GLY. (Don't try this at home or you might alter the "lib/all_amino94.lib". In general, we would not suggest modifying any standard libraries, rather, one should create a new UNIT for practice.)
restrainTorsion unit a b c d force phi multiplicity
(in degrees), and a periodicity of multiplicity
(see the restrainBond command for an example of this
command).
saveAmberParm unit topologyfilename coordinatefilename
In the following example, the topology and coordinates from the all_amino94.lib UNIT ALA are generated:
saveAmberParmPol unit topologyfilename coordinatefilename
saveAmberParmPert unit topologyfilename coordinatefilename
Save the AMBER/SPASMS 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 topology files and coordinate files that are identical in format to those produced by AMBER PARM and can be read into AMBER gibbs and SPASMS for perturbation calculations.
saveAmberParmPolPert unit topologyfilename coordinatefilename
saveOff object filename
savePdb unit filename
scaleCharges container scale_factor
select object
variable = sequence list
set container parameter object
For ATOMs:
For RESIDUEs:
For UNITs:
setBox unit [ buffer OR buffer_xyz_list ]
solvateBox solute solvent buffer [ iso ] [ closeness ]
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 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 cubic, with the shortest box clearance = buffer. 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 how close, in angstroms, solvent ATOMs can come to solute ATOMs. The default value of the closeness argument is 1.0. Smaller values allow solvent ATOMs to come closer to solute ATOMs. The criterion for rejection of overlapping solvent RESIDUEs is if the distance between any solvent ATOM to the closest solute ATOM is less than the sum of the ATOMs VANDERWAAL distances multiplied by the closeness argument.
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.
In this example, it is assumed that the file water.lib, containing WATBOX216, has been loaded already (as is done by the default leaprc):
Again, note that the density of 0.601 g/cc points to the need for constant pressure equilibration. (See the discussion of equilibration in the Q&A section of the amber web.)
solvateCap solute solvent position radius [ closeness ]
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 how close, in angstroms, solvent ATOMs can come to solute ATOMs. The default value of the closeness argument is 1.0. Smaller values allow solvent ATOMs to come closer to solute ATOMs. The criterion for rejection of overlapping solvent RESIDUEs is if the distance between any solvent ATOM to the closest solute ATOM is less than the sum of the ATOMs VANDERWAAL's distances multiplied by the closeness argument.
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 ]
Note the larger number of waters added, compared to solvateBox; in the case of this solute and choice of buffer, the overall box size is increased by about 10 angstroms in each direction.
solvateOct solute solvent buffer [iso] [ closeness ]
solvateShell solute solvent thickness [ closeness ]
source filename
"source"ing it will produce the output listing shown below.
transform atoms, matrix
3 )
or ( 4 
4 ) matrix represented by the
nine or sixteen NUMBERS in the LIST
of LISTs matrix.
The general matrix looks like:
The matrix elements represent the intended symmetry operation. For example, a reflection in the (x, y) plane would be produced by the matrix:
This reflection could be combined with a six angstrom translation along the x-axis by using the following matrix.
In the following example, wrB is transformed by an inversion operation:
translate atoms direction
Example:
verbosity level
zMatrix object zmatrix
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.
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.
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.
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 object. 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.
There is no order 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. (See the add command for an example of the zMatrix command.)