Îúíþ8 БµT‘µ__text__TEXTzTè·Œ€__data__DATAzÎ __cstring__TEXT€ì­Ô __picsymbolstub2__TEXTlµÀ·HÄ€__la_sym_ptr2__DATA…µÙ·xÄ__textcoal_nt__TEXT‰µÝ· @ˆÄÄÄ\ P€ÄU‰åSƒìèôÿÿÿƒt‰D$ƒH‰$èHµƒT‰D$ƒ ‰$è0µƒ4 ‰D$ƒ‰$赃‰D$ƒE‰$赃T‰D$ƒ‰$èè´ƒ‰D$ƒ¼‰$èдƒÔ‰D$ƒ_‰$踴ƒt‰D$ƒ·‰$è ´ƒÔ‰D$ƒ²‰$舴ƒÔ‰D$ƒö‰$èp´ƒ‰D$ƒK‰$èX´ƒt‰D$ƒ1‰$è@´ƒT‰D$ƒì‰$è(´ƒô‰D$ƒÀ‰$è´ƒÔ‰D$ƒó!‰$èø³ƒ"‰D$ƒ"#‰$èೃ4#‰D$ƒ‚$‰$èȳƒ”$‰D$ƒ&‰$è°³ƒ4&‰D$ƒE(‰$蘳ƒT(‰D$ƒÞ(‰$耳ƒô(‰D$ƒÜ)‰$èh³ƒô)‰D$ƒÛ*‰$èP³ƒô*‰D$ƒ‚+‰$è8³ƒ”+‰D$ƒü+‰$è ³ƒ,‰D$ƒ2-‰$賃T-‰D$ƒC/‰$èð²ƒT/‰D$ƒ€0‰$èزƒ”0‰D$ƒ\1‰$èÀ²ƒt1‰D$ƒ99‰$訲ƒT9‰D$ƒŒ9‰$貃”9‰D$ƒ¹;‰$èx²ƒÔ;‰D$ƒ(>‰$è`²ƒT>‰D$ƒ7?‰$èH²ƒT?‰D$ƒÙC‰$è0²ƒôC‰D$ƒE‰$貃´E‰D$ƒÉF‰$貃ÔF‰D$ƒèG‰$è豃ôG‰D$ƒ¨H‰$èбƒÔH‰D$ƒ‚I‰$踱ƒ”I‰D$ƒ!J‰$è ±ƒ/J‰D$ƒGJ‰$舱ƒTJ‰D$ƒÜK‰$èp±ƒôK‰D$ƒÓL‰$èX±ƒôL‰D$ƒIN‰$è@±ƒtN‰D$ƒmQ‰$è(±ƒ”Q‰D$ƒ U‰$豃4U‰D$ƒÐV‰$èø°ƒôV‰D$ƒ1Z‰$èà°ƒTZ‰D$ƒø[‰$èÈ°ƒ\‰D$ƒt]‰$è°°ƒ”]‰D$ƒ¶]‰$蘰ƒÔ]‰D$ƒ4`‰$耰ƒT`‰D$ƒ…c‰$èh°ƒ”c‰D$ƒ1d‰$èP°ƒTd‰D$ƒØd‰$è8°ƒôd‰D$ƒ–e‰$è °ƒ´e‰D$ƒLEaPVar name map will only be applied for the appropriate terminal residue. The `leaprc' file included with the distribution contains default mappings. addPdbResMap clearPdbAtomMap Clear the Name Map used for ``second-chance'' mapping of atom names in PDB files to atoms within residue UNITs. See addPdbAtomMap. clearPdbAtomMap clearPdbResMap Clear the Name Map used to map residue names in PDB files to variable names within LEaP. See addPdbResMap. clearPdbResMap displayPdbAtomMap Display the Name Map used for ``second chance'' mapping of atom names in PDB files to atoms within residue UNITs. See addPdbAtomMap. displayPdbAtomMap displayPdbResMap Display the Name Map used to map residue names in PDB files to variable names within LEaP. See addPdbResMap. displayPdbResMap savePdb unit filename UNIT _unit_ STRING _filename_ Write UNIT to the file _filename_ as a PDB format file. savePdb select obj UNIT/RESIDUE/ATOM _obj_ Sets the SELECT flag on all ATOMs within _obj_. See the 'deSelect' command. select 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. sequence 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 scaleCharges 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_. The possible variables for "set default" are: 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) PBRadii "bondi" use Bondi radii for generalized Born "mbondi" use H-modified Bondi radii (default) "mbondi2" use H(N)-modified Bondi radii "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 The more useful parameters for each type of _container_ are: container attributes values UNIT name STRING head, tail ATOM [e.g. unit.1.1] restype "protein" "nucleic" "saccharide" "solvent" "undefined" [sets all residues in UNIT] 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}] set setBox vdw OR centers [ buffer OR buffer_xyz_list ] The setBox command adds a periodic box to the 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 the entire atoms or just the 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 variable, which extends either type of box by an arbitrary amount. setBox 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. solvateBox 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. solvateOct 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. solvateCap 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. solvateDontClip 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. solvateShell measureGeom atom1 atom2 [ atom3 atom4 ] ATOM _atom1_ _atom2_ _atom3_ _atom4_ Measure the distance, angle or torsion between two, three or four ATOMs, respectively. measureGeom listOff library STRING _library_ List the UNITs/PARMSETs stored within the Object File Format file named _library_. listOff deleteOffLibEntry library entry STRING _library_ STRING _entry_ Delete _entry_ from the Object File Format file named _library_. deleteOffLibEntry 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. source 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_. translate 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). transform 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. matchVariables 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. verbosity 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. zMatrix UNIT A collection of ATOMs, perhaps grouped into one or more RESIDUEs. In combination with PARMSET parameters, a UNIT contains all the information needed for a simulation. RESIDUE A collection of ATOMs, some of which may be designated as "connect"ing. A RESIDUE has a chemical type such as "protein," "nucleic," "saccharide," "solvent," or "undefined." ATOM Has a name, a force field type, an element type, a charge, perturbed name-types-charge, and a position. PARMSET A collection of force field parameters. When a UNIT is associated with parameters, the PARMSETs that have been loaded are searched in order of most recently loaded to first loaded. LIST A sequence of objects within '{' and '}', delimited by spaces. LISTs can contain other lists. STRING A series of any characters within quotes or alphanumeric characters preceded by a '$'. Also, a string of alpha- numeric characters standing alone is interpreted as a STRING if it does not correspond to a variable name. NUMBER A number, treated as floating point double precision. _types_The command-line options for starting tleap and xleap are: -h List these options. -s Ignore any leaprc startup file. -I {dir} Add {dir} to search path. -f {file} Source {file}. The tleap and xleap shell scripts automatically provide -I$AMBERHOME/dat -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/cmd where $AMBERHOME/dat contains 'parm.dat' force field files, $AMBERHOME/dat/leap/lib contains residue libraries and $AMBERHOME/dat/leap/cmd contains the default leaprc and other scripts. _cmd_options_èJÿÿ‹ÿâ€Pé{Jÿÿyµ‹$Ë$Ãph¤^µ¡ ^¤@³¡ XP¤7³¡ F¤ ®¡ @8¤ ®¡ .¤ £¡ ( ¤–£¡ ¤ ¢¡ ¤¢¡ þ¤À ¡ ø𤱠¡ æ¤ ž¡ àؤ ž¡ Τ ¡ ÈÀ¤¡ ¶¤à›¡ °¨¤Â›¡ ž¤›¡ ˜¤Úš¡ †¤@š¡ €x¤"š¡ n¤`™¡ h`¤@™¡ V¤@•¡ PH¤•¡ >¤€’¡ 80¤u’¡ &¤ ‹¡ ¤ùŠ¡ ¤`†¡ ¤F†¡ ö¤|¡ ðè¤è{¡ Þ¤Ày¡ ØФ¥y¡ Ƥ m¡ À¸¤m¡ ®¤`k¡ ¨ ¤Dk¡ –¤Àg¡ ˆ¤©g¡ ~¤ g¡ xp¤g¡ f¤`f¡ `X¤Hf¡ N¤Àe¡ H@¤¢e¡ 6¤e¡ 0(¤äd¡ ¤`d¡ ¤=d¡ ¤ c¡ ø¤‘c¡ î¤``¡ èà¤@`¡ Ö¤à]¡ ÐȤÂ]¡ ¾¤ ]¡ ¸°¤€]¡ ¦¤ \¡  ˜¤\¡ Ž¤`Z¡ ˆ€¤=Z¡ v¤W¡ ph¤ÜV¡ ^¤@U¡ XP¤,U¡ F¤ Q¡ @8¤yQ¡ .¤€N¡ ( ¤UN¡ ¤M¡ ¤ßL¡ þ¤L¡ øð¤èK¡ æ¤`J¡ àؤSJ¡ Τ;J¡ ÈÀ¤-J¡ ¶¤ I¡ °¨¤ŽI¡ ž¤àH¡ ˜¤´H¡ †¤H¡ €x¤ôG¡ n¤àF¡ h`¤ÕF¡ V¤ÀE¡ PH¤œE¡ >¤D¡ 80¤åC¡ &¤`?¡ ¤C?¡ ¤`>¡ ¤4>¡ ö¤à;¡ ðè¤Å;¡ Þ¤ 9¡ ØФ˜9¡ Ƥ`9¡ À¸¤E9¡ ®¤€1¡ ¨ ¤h1¡ –¤ 0¡ ˆ¤Œ0¡ ~¤`/¡ xp¤O/¡ f¤`-¡ `X¤>-¡ N¤ ,¡ H@¤,¡ 6¤ +¡ 0(¤Ž+¡ ¤+¡ ¤ç*¡ ¤*¡ ø¤è)¡ î¤)¡ èà¤ê(¡ Ö¤`(¡ ÐȤQ(¡ ¾¤@&¡ ¸°¤&¡ ¦¤ $¡  ˜¤Ž$¡ Ž¤@#¡ ˆ€¤.#¡ v¤ "¡ ph¤ÿ!¡ ^¤à¡ XP¤Ì¡ F¤¡ @8¤ø¡ .¤`¡ ( ¤=¡ ¤€¡ ¤W¡ þ¤ ¡ ø𤡠æ¤à¡ àؤ¾¡ Τà¡ ÈÀ¤Ã¡ ¶¤€¡ °¨¤k¡ ž¤à¡ ˜¤È¡ †¤ ¡ €x¤¡ n¤`¡ h`¤Q¡ V¤ ¡ PH¤¡ >¤@ ¡ 80¤ ¡ &¤`¡ ¤T¡ ¤€¡   ¤…µ¡qµ¤…µ¡qµ !€‰µ €µR9_HTInit___i686.get_pc_thunk.bx___i686.get_pc_thunk.axdyld_stub_binding_helper_HelpAdd