This section focuses on concepts necessary to employ LEAP to produce input files for the AMBER molecular mechanics programs. First we discuss loading force field parameter files (PARMSETs) and residue libraries, and then the general strategy for using LEAP to create the coordinates and parameters necessary to run AMBER. The user should refer to the "Examples" section and the tutorials in under the "Web" part of the AMBER source tree for detailed analyses of utilizing LEAP for specific tasks.
There are two AMBER force fields, Weiner et al. 1984, 1986
and Cornell et al. 1995. The associated files happen to be
named "91" and "94" respectively. Each force field consists of
residue definitions in one or more files, and an accompanying
parameter file, or PARMSET. The residue definitions and PARMSET
must be compatible. The newer Cornell et al. force field is
loaded by the default leaprc file. A
$AMBERHOME/dat/leap/cmd/leaprc.ff91 file is provided
for loading the Weiner et al. force field;
to use it, one would copy this file to leaprc
in the current directory. You never want to have
both force fields (or parts of both) loaded at once,
because they use incompatible and overlapping atom
type definitions.
The mechanism for loading PARMSETs is the
loadAmberParams command. The Weiner et al.
PARMSET file for LEAP is parm91X.dat; the Cornell
et al. one is parm94.dat. The default leaprc
loads Cornell et al. as UNIT "parm94," while
leaprc.ff91 loads Weiner et al. as "parm91."
The list command will show the PARMSET(s) that have
been loaded along with all other objects currently existing
in LEAP.
In addition to one of the standard PARMSETs, one may need to
load extra parameters, either for residues not contained in these
basic force fields, or in order to override standard parameters.
This is done by making a frcmod file in a normal text editor
and loading that as well (using loadAmberParams). The most
recently-loaded parameters take precedence when there is a duplicate
definition of e.g. an atom type, so a frcmod file can be used
to alter standard parameters without the risk of modifying the
standard file and losing track of what was changed.
NOTE that the nonbonded parameters in PARMSETs
must be of the form r* and 
. LEAP will
not read nonbonded parameters of the form "A & C".
Also, for every atom type "mass" definition in the
parameter set, there must also exist a nonbonded
parameter for that atom type. LEAP ignores
polarizability values from AMBER PARM parameter sets.
When LEAP needs force field parameters for commands
like saveAmberParm or saveAmberParmPert,
it searches through the list of PARMSETs that are
currently loaded from the most recently loaded to the
oldest. As soon as LEAP finds a parameter
that matches the configuration of atom types
for which it is looking, it stops searching the
PARMSET list.
Parameters for torsional terms are found by searching each loaded PARMSET in turn. Specific torsional parameters take precedence over general ones (i.e. parameters having wild-card atoms). Only an exact match will prevent searching all the PARMSETs.
A set of residue libraries is provided for each force field;
the file names include "91" for Weiner et al. and
"94" for Cornell et al.. The latter ones are loaded
by the default leaprc file. One can see a list of
all the loaded residues using the list command.
In this section, we list the UNITs found in the libraries
and their names and aliases. When a UNIT is
distributed with LEAP, all of the force field
parameters needed to define the UNIT within
AMBER are also found in the PARMSETs.
The following amino acid UNITs and their aliases are defined in the LEAP libraries.
+-------------------------------------------------+
| Group or residue Residue Name, Alias |
+-------------------------------------------------+
|Acetyl beginning group ACE |
|Amine ending group NHE |
|N-methylamine ending group NME |
|Alanine ALA |
|Arginine ARG |
|Asparagine ASN |
|Aspartic acid ASP |
|Cysteine CYS |
|Cystine, S--S crosslink CYX |
|Glutamic acid GLU |
|Glutamine GLN |
|Glycine GLY |
|Histidine, delta H HID |
|Histidine, epsilon H HIE |
|Histidine, protonated HIP |
|Isoleucine ILE |
|Leucine LEU |
|Lysine LYS |
|Methionine MET |
|Phenylalanine PHE |
|Proline PRO |
|Serine SER |
|Threonine THR |
|Tryptophan TRP |
|Tyrosine TYR |
|Valine VAL |
+-------------------------------------------------+
The UNIT/RESIDUE names and aliases listed above correspond to the AMBER all atom force field. (The Weiner et al. united atom force field has not been adapted for LEAP.) For each of the amino acids found in the LEAP libraries, there has been created an n-terminal and a c-terminal analog. The n-terminal amino acid UNIT/RESIDUE names and aliases are prefaced by the letter N (e.g. NALA) and the c-terminal amino acids by the letter C (e.g. CALA}. If the user models a peptide or protein within LEAP, they may choose one of three ways to represent the terminal amino acids. The user may use 1) standard amino acids, 2) protecting groups (ACE/NME), or 3) the charged c- and n-terminal amino acid UNITs/RESIDUEs. If the standard amino acids are used for the terminal residues, then these residues will have incomplete valences. These three options are illustrated below:
The default for loading from PDB files is to use
n- and c-terminal residues; this is established by
the addPdbResMap command in the default
leaprc files. To force incomplete valences
with the standard residues, one would have to define
a sequence (" x = { ALA VAL SER PHE }")
and use loadPdbUsingSeq, or use clearPdbResMap
to completely remove the mapping feature.
It should be noted that by convention amino acid sequences are written starting with the n-terminus. This same convention is used in LEAP, dictated by the atom order in the residue libraries.
Histidine can exist either as the protonated species or as a neutral species with a hydrogen at the delta or epsilon position. For this reason, the histidine UNIT/RESIDUE name is either HIP, HID, or HIE (but not HIS). The default "leaprc" file assigns the name HIS to HID. Thus, if a PDB file is read that contains the residue HIS, the residue will be assigned to the HID UNIT object. This feature can be changed within one's own "leaprc" file.
The AMBER force fields also differentiate between the
residue cysteine (CYS) and the similar residue which
participates in disulfide bridges, cystine (CYX). The
user will have to explicitly define, using the
crossLink command, the disulfide bond for a
pair of cystines, as this information is not
read from the PDB file. In addition, the user will
need to load the PDB file using the loadPdbUsingSeq
command, substituting CYX for CYS in the sequence wherever
a disulfide bond will be created.
The following are defined for the 1994 force field.
+---------------------------------------+ |Group or residue Residue Name, Alias | +---------------------------------------+ |Adenine DA,RA | |Thymine DT | |Uracil RU | |Cytosine DC,RC | |Guanine DG,RG | +---------------------------------------+
The "D" or "R" prefix can be used to distinguish between deoxyribose and
ribose units; with the default leaprc file, ambiguous residues are
assumed to be deoxy. Residue names like "DA" can be followed by a "5" or
"3" ("DA5", "DA3") for residues at the ends of chains; this is also the
default established by addPdbResMap, even if the "5" or "3" are not
added in the PDB file. The "5" and "3" residues are "capped" by a hydrogen;
the plain and "3" residues include a "leading" phosphate group.
Neutral residues capped by hydrogens are end in "N," such as "DAN."
Miscellaneous Residue unit/residue name _ TIP3P water molecule WAT, HOH, IP3 Periodic box of TIP3P water WATBOX216 Cesium cation Cs+ Potassium cation K+ Rubidium cation Rb+ Lithium cation Li+ Sodium cation Na+ or IP Chlorine Cl- or IM Large cation IB"IB" represents a solvated monovalent cation (say, sodium) for use in vacuum simulations. The cation UNITs are found in the files "ions91.lib" and "ions94.lib", while the water UNITs are in the file "water.lib". The default
leaprc file
assigns the variables HOH and IP3 to the WAT UNIT
found in the OFF library file. Thus, if a PDB file is
read and that file contains either the residue name HOH or
IP3, the WAT UNIT will be substituted. (Note that PDB
residue names are restricted to 3 characters.)
A periodic box of 216 waters (WATBOX216) is provided in the file "water.lib". The box measures 18.774 angstroms on a side. This box of waters has been equilibrated by a Monte Carlo simulation. It is the UNIT that should be used to solvate systems with TIP3P water molecules within LEaP. It has been provided by W. L. Jorgensen.
In order to prepare a molecule within LEAP for AMBER, three basic tasks need to be completed.
Before start-up, LEAP contains no objects. In
the default configuration, standard PARMSET and
UNIT residue libraries for the Cornell et al.
force field are loaded by the default leaprc
file in $AMBERHOME/dat/leap/cmd/. This file can be consulted
or copied as a template for constructing a useful
work environment.
The saveOff command is used to save constructed
UNITs to libraries, and frcmod-style PARMSETs are
constructed using a normal text editor. Both may
be loaded to prepare for a session using loadOff
and \loadAmberParams respectively.
Objects are loaded into LEAP either by the user typing in load commands interactively, or by placing appropriate load commands within a "leaprc" start-up file in the working directory.
There are several different methods of constructing
molecules or UNITs within LEAP. If the user has
an AMBER PREP file, the structure may be read in
using the loadAmberPrep command. PDB files
are read into LEAP using the loadPdb or
loadPdbUsingSeq commands. It is also possible
to construct a molecule structure manually using the
zMatrix command or (most commonly) the xleap
edit command. The user may use any combination
of these methods to make molecules. Once a UNIT is
created, it can be stored in an OFF library for
subsequent use. Thus, if a user is building a
polypeptide which includes one novel amino acid,
they would load the OFF library of standard amino
acids and create the novel amino acid residue through one
of the abovementioned methods. This nonstandard amino
acid residue UNIT could then be stored and reloaded
at the beginning of future sessions.
Let us examine several methods of constructing a water molecule within LEAP. One such method would be to build a water UNIT, which we will call WAT, by utilizing a Z-matrix input for structure. Note that this method is probably only convenient if one already has such a matrix; normally it is easier to draw the new residue usinthe Unit Editor.
In the following example, presented as if it were
a special leaprc, the user constructs WAT by creating
ATOMs, then a RESIDUE, and finally the WAT UNIT. A
structure is applied to the UNIT by using internal
coordinates given by a Z-matrix. In this illustration,
the user does not define any head or tail
atoms for the RESIDUE or any connect atoms for
the UNIT. This is because WAT is not a residue in
the chemical sense; the WAT UNIT will never be
used as a substituent or monomer. Once the WAT
UNIT is created, a topology file and a coordinate
file are generated for molecular mechanics
calculations. In this and subsequent illustrations,
all input command lines are prefaced by the
characters "> ". The program output found in
these listings is not prefaced by the characters.
Another method of constructing a molecule is to use a PDB file. This time, rather than first building the molecule atom-by-atom and adding bonds to create a template, we just load the PDB file and begin work on that.
The user may want to model a molecule for which a PDB file exists and a LEAP UNIT has already been created and stored in an OFF library. In this case, it is only necessary to load a PARMSET, the UNIT, and PDB file into LEAP. It is important to replace the coordinates of the UNIT with those of the PDB file in order to ensure that the molecular structure assumes the conformation of interest to the user. To understand this last point, consider the construction of a protein. When the UNITs in LEAP are joined together to form the protein sequence, the resulting structure is linear. Replacing the Cartesian coordinates of the UNITs will allow the proper tertiary protein structure to be modeled. The following example illustrates this procedure:
If an AMBER PREP file exists for the water molecule it can be used to create the water UNIT within LEAP. When the PREP file is loaded into LEAP, 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.
We have illustrated several methods of constructing a water molecule within LEAP. By far, the most convenient method is the one which we will now discuss. If the user runs the xleap program, the molecule can be created quite easily graphically within the Unit Editor.
After the xleap program is started and a PARMSET
is loaded, the user can enter the Unit Editor with
the edit command. If the command argument
(WAT) is not an existing UNIT, a new RESIDUE and
UNIT will be created and the program will display
a Unit Editor for WAT.
The first objective is to draw and build the molecule.
In the Control Window is a button named draw.
The user should select this button with the left
mouse button. The Viewing Window will now be set
to the Draw mode. The user should then select
the O (oxygen) element button in the
Control Window. This will set the drawing element
type to oxygen. The Draw mode mouse
button (left button) is depressed and clicked
anywhere on the screen. The user can then
release the mouse button. Now the user can
select the Unit pulldown command:
Add H & Build. Two hydrogen ATOMs will
be added to the oxygen and the molecular structure
will be generated using the geometry builder rules.
The user may want to rotate the molecule, using the
middle mouse button, to confirm that the geometry
is correct.
Next, the user needs to edit the ATOMs.
The entire molecule should be selected by pressing
the Manipulation Select option and then pressing
the Select mode mouse button (left button)
anywhere in the Viewing Window background and
dragging the mouse until the select box
encompasses the molecule. The mouse button can
then be released. The user should then choose
the Edit selected items command from the
Edit pulldown. An Atom Properties Editor
will appear.
The Unit Editor has already assigned names
to the ATOMs and if desired, the user can
change the names. In order for correct AMBER
force field parameters to be assigned, the user
must define the oxygen and hydrogen ATOM types
as "OW" and "HW", respectively. The user should
also assign electrostatic point charges to each
ATOM. The Atom Properties Editor can then be
closed by choosing the "Save and quit" command
in the Table pulldown. The UNIT has been
created and the user can return to the xleap
Universe Editor. Note that this WAT residue
does not correspond to the TIP3P WAT residue
that is loaded from water.lib since it
lacks an H-H bond (used for keeping the molecule
rigid with SHAKE).
Once the UNIT is constructed, it should be examined
using the check command. The UNIT may also
be augmented in many ways, including adding
counterions, restraints, or solvents.
Finally, the user needs to obtain topology and coordinate
files. These files are used as input for AMBER.
These two files are created by the saveAmberParm
command. If the user constructed a UNIT to be used in
a Free Energy Perturbation calculation, then the
saveAmberParmPert command should be used instead.