Shell Scripts and Awk Programs

1. cartopdbq

 
Usage
: cartopdbq lig.car > lig.pdbq

Converts from Biosym InsightII ".car" format to PDBQ format

• check-qs

 
Usage
: check-qs lig

Needs:
 lig.pdbq

Creates:
 lig.err

Checks partial atomic charges in PDBQ file; any non-integral charges are reported.

• checkqs

 
Usage
: checkqs lig

Needs:
 lig.pdbq

Creates:
 lig.err

Sorts the input PDBQ file by residue number before running the result through check-qs .

• clamp

 
Usage
: clamp grid.map > grid.map.NEW

Clamps any AutoGrid map values that exceed ECLAMP (normally set to 1000.0)

• cnvmol2topdbq

 
Usage
: cnvmol2topdbq lig.mol2 > lig.pdbq
Needs:
 lig.mol2
Creates:
 lig.pdbq

This converts from (fixed format) Tripos SYBYL mol2 fiormat into PDBQ format, but stores all the residues' chain-IDs specified by the SUBSTRUCTURE records in the mol2 file. These chain-IDs are then output when the PDBQ lines are written.

• deftors

 
Usage
: deftors lig.mol2

Creates
: lig.pdbq
, lig.err

Sets up rotatable bonds for AutoDock . This script launches AutoTors , with the -A +15.0, -a, -h and -m flags; it also checks the charges in the output PDBQ file, with check-qs .

• dpf3gen

 
Usage
: dpf3gen lig.pdbq > lig.dpf

This is normally used by mkdpf3 , so you should not use this script by hand.

It generates a pre-cursor to a default AutoDock docking parameter file. You must edit the file before using it. This reads in the small molecule PDBQ file, detects all atom types present in the lig.pdbq; and creates a docking parameter file for AutoDock . Note the user must replace the tags <lig> and <macromol> by appropriate filename stems.

This uses equilibrium separations and well depths to define pairwise energy potentials, rather than coefficients.

• get-coords

 
Usage: 
get-coords lig.vol > lig.txt

This is used as part of prepare , prepare-gpf+dpf , prepare II and prepare III . It takes the .vol file created by pdb-volume and creates a line that can be used in the grid parameter file to specify the center of the maps.

• get-docked

 
Usage
: get-docked lig.macro.dlg
Creates
: lig.macro.dlg.pdb

This extracts the docked records from a docking log file. This is very useful when wanting to view the results of a docking in a molecular modelling program or molecular viewer. It is essentially the same as the ` dockedtopdb ' awk program.

• gethis

 
Usage
: gethis lig.macro.dlg

• This outputs the histogram from the confomational analysis section of the AutoDock log file, lig.macro.dlg , and writes it to the screen.
• getready

 
Usage
: getready lig.pdb

Needs:
 	pdbinfo, pdbsplitchains, pdbwaters, pdbdewater

Creates:
 lig.info, lig_.atm.pdb, lig_.het.pdb, lig_.wat.pdb

• This is a very useful script to get started. It will split a PDB file into separate files, each containing a different chain, and will split each of these chains into ATOM, non-water HETATM and water containing PDB files. Also the .info file is a useful summary description of the PDB file.
• gpf3gen

 
Usage
: gpf3gen lig.pdbq[s] > lig.gpf

This is used by mkgpf3 , and should not be used by hand; otherwise the user must edit certain tags by hand before this can be used by AutoGrid .

This generates a precursor to a grid parameter file. It takes lig.pdbq as its input file, detects all atom types present, and creates the properly formatted parameter file for AutoGrid . It uses equilibrium separations and well depths to define pairwise energy potential. It also assigns atomic solvation parameters, based on Stouten, P.F.W., FrÖmmel, C., Nakamura, H., and Sander, C. (1993), "An effective solvation term based on atomic occupancies for use in protein simulations", Molecular Simulation , 10 , 97-120.

• histable

 
Usage
: histable lig.macro.dlg
Creates
: lig.macro.dlg.tbl

This extracts the histogram from the docking log file, and counts all the `#' symbols, writing the result in a table file. This is suitable for input to a variety of graph drawing programs and spreadsheets.

• job3

 
Usage
: job3 lig.macro > lig.macro.joblog &

Launches a single AutoDock 3.0 job. It assumes that " lig.macro.dpf " exists, and executes AutoDock using the arguments:

 
autodock3 -p lig.macro.dpf -l lig.macro.dlg

You must edit this script the first time you use it, so that the environment variables $root, $bin and $sh are correctly set equal to, respectively: the path to the root of AutoDock tree, the architecture-dependent binary subdirectory and the Unix scripts subdirectory. The file lig.macro.joblog contains the output from the job script.

• makebox

 
Usage
: makebox macro.gpf >! macro.gpf.box.pdb

Creates
: macro.gpf.box.pdb

• This creates a PDB file from the grid parameter file `macro.gpf', that shows how big and where the grid box will be when AutoGrid calculates the grid maps. You can use this `box molecule' to help refine the center and number of grid points in the grid maps, before you run AutoGrid.

If you colour the `box molecule' by atom type, i.e. red for oxygen, green for carbon, and blue for nitrogen, then the edges of this box will be coloured-coded to indicate the Cartesian axes. R,G,B will correspond to x,y,z, respectively. Your molecule viewer must obey the CONECT records in the ` macro.gpf.box.pdb ' file, even though the corresponding bonds may appear too long, otherwise the edges of the grid box will not be displayed.

• mkbox

 
Usage
: mkbox macro.gpf >! macro.gpf.box.pdb

Creates
: macro.gpf.box.pdb

This is very similar to ` makebox ', except that this puts a phosphorus atom at the minimum x , minimum y and minimum z coordinates of the box. This helps to convey which directions are +x, +y and +z . Once again, if oxygen is red, carbon is green and nitrogen is blue, then R,G,B will correspond to x,y,z, respectively.

• mkdlgfld

 
Usage
: mkdlgfld lig.macro.dlg

Needs
: lig.macro.dlg

Creates
: lig.macro.dlg.fld

Only needed for AVS users.

This extracts the "AVSFLD" records from an AutoDock log file, and puts them in lig.macro.dlg.fld. These "AVSFLD" descriptors must be removed before the file can be used in AVS.

• mkdpf3

 
Usage
: mkdpf3 lig.pdbq macromol.pdbqs

Needs
: dpf3gen, dpf3gen.awk (AWK program)
Creates
: lig.macro.dpf

This creates a default docking parameter file for AutoDock 3.0; it needs the ligand in PDBQ format and the macromolecule in PDBQS format. It uses the script dpf3gen , which in turn calls the awk program ` dpf3gen.awk '. The lig.macro.dpf docking parameter file is based on the atom types detected in the input lig.pdbq file. See dpf3gen above.

• mkgpf3

 
Usage
: mkgpf3 lig.pdbq macromol.pdbqs
Needs
: gpf3gen, gpf3gen.awk (AWK program), 
pdbcen (AWK program)
Creates
: macro.gpf

This creates a default grid parameter file for AutoGrid 3.0; it needs gpf3gen.awk and pdbcen , both awk programs. See gpf3gen above.

• mol2fftopdbq

 
Usage
: mol2fftopdbq lig.mol2 > lig.pdbq

Needs:
 lig.mol2

Creates:
 lig.pdbq

Converts from free formatted SYBYL mol2 into AutoDock PDBQ format. Chain-IDs specified in the mol2 file by the SUBSTRUCTURE records are incorporated into the PDBQ file.

• mol2topdbq

 
Usage
: mol2topdbq lig.mol2

Needs:
 lig.mol2

Creates:
 lig.pdbq

Converts from fixed-format SYBYL mol2 into AutoDock PDBQ format, and automatically names the output based on the stem of the input mol2 file. Do not use " mol2topdbq lig.mol2 > lig.pdbq ", because " lig.pdbq " is automatically created.

• mol2topdbqs

 
Usage
: mol2topdbqs lig.mol2

Needs:
 lig.mol2

Creates:
 lig.pdbqs

• Converts from SYBYL mol2 format into AutoGrid 3.0 PDBQS format, by calling mol2topdbq then running addsol on the intermediate PDBQ file. Like mol2topdbq , it also removes any lone pairs (using " rem-lp "), and automatically names the output based on the stem of the input mol2 file. There is no need to use " mol2topdbq lig.mol2 > lig.pdbq ", because " lig.pdbqs " is automatically created.
• pdbcen

 
Usage
: pdbcen lig.pdb
Creates
: a "gridcenter" line in AutoGrid GPF format, holding the x,y,z coordinates of the molecule.

This calculates the center of a molecule supplied in PDB format, and outputs a line holding the x,y,z coordinates of the molecule for inclusion in an AutoGrid 3.0 grid parameter file (GPF).

• pdb-center

 
Usage
: pdb-center [ lig.pdb | lig.pdbq ] > lig2.pdb

Calculates the center of mass of each residue; writes these coordinates out using REMARK records.

• pdb-center-all

 
Usage
: pdb-center-all [ lig.pdb | lig.pdbq ] > lig2.pdb

Calculates the center of mass of each residue; writes these coordinates out using REMARK records.Also calculates the center of all the residues.

• pdb-distance

 
Usage
: pdb-distance macro.pdb

The first line of the macro.pdb file defines the center of the distance profile. It is just a copy of the line containing the atom of interest, which will be the origin for the distance calculations. However, it must have the ATOM or HETATM record replaced with a non-PDB tag, `FROM'. The x,y,z coordinates in this FROM line will then be used to calculate the distance to the center of each residue in the protein. Finally, this awk program outputs a bar chart using `#' symbols, showing the distance from this point to each residue. This can be useful to identify all the residues nearest a particular ligand atom, or near an active site.

• pdbdewater

 
Usage
: pdbdewater macro.pdb >! macro.dry.pdb

This removes any water records from a PDB file.

• pdbinfo

 
Usage
: pdbinfo macro.pdb

Builds a summary of the contents of a PDB file.

• pdb-volume

 
Usage
: pdb-volume [ lig.pdb | lig.pdbq ] > lig2.pdb

Calculates the center of mass of each residue. Writes out REMARKs showing these coordinates. Draws ASCII diagram showing volume extents of each residue.

• pdbqtobnd

Usage : pdbqtobnd lig
Needs: lig.pdbq
Creates: lig.bnd

Creates " lig.bnd " from the existing " lig.pdbq " ligand PDBQ file. Note this script needs just the stem of the file name. This script executes " pdbqtoatm " and " atmtobnd ": the latter is an executable, not a script, so it must be compiled for each architecture and operating system used.

• pdbqtopdb

 
Usage
: pdbqtopdb lig.pdbq > lig.pdb

Converts from AutoDock PDBQ to PDB format.

• pdbsplitchains

 
Usage
: pdbsplitchains macro.pdb

Creates separate PDB files that contain each of the chains in macro.pdb . The chain IDs are used to name the new PDB files. If there is no chain ID, the underscore character, `_' is used.

• pdbtoatm

Usage : pdbtoatm lig.pdbq > lig.atm

This creates a Connolly ATM formatted file " lig.atm " from the ligand PDBQ file, " lig.pdbq ". This is used to create input for the utility program atmtobnd to generate a bond connectivity file.

• pdbdewaters

 
Usage
: pdbwaters macro.pdb > macro.wet.pdb

• Extracts the waters from macro.pdb into macro.wet.pdb .
• prepare

 
Usage:
 prepare m s

where : m.pdb and s.pdbq contain the receptor and ligand respectively. Prepare performs the following eight steps. The macromolecule ` .pdb ' filename stem is represented by " m ", and the ligand ` .pdbq ' filename stem by "s":

1. Extracts all ATOM and TER records from m.pdb into m.enz;
2. Renumbers residues to avoid problems in protonate -step;
3. Adds polar hydrogens to m.enz , creating m.polH ;
4. Somewhat crudely assigns partial atomic charges to m.polH , creating m.pdbq ;
5. Checks charges in m.pdbq , all errors held in m.err ;
6. Creates s.gpf , a parameter file for AutoGrid , based on ligand file s.pdbq ;
7. Creates s.vol , a volume dimensions file; and finally,
8. Creates s.dpf , a parameter file for AutoDock, based on ligand file s.pdbq ;

Its arguments are the stem of the filename of the macromolecule ` .pdb ' file and that of the ligand PDBQ file. See the flowchart below for more details. It shows what files are created by ` prepare ', and which scripts or programs are used. Steps 1.-4. are better carried out with a reliable molecular modeling system: these steps can produce some odd results unless carefully checked.

The user must check the m.err error file to ensure there are no non-integral charges, either on any residue in the macromolecule, or on the macromolecule as a whole. If there are, then the user must repair the m.pdbq file. This problem can arise if there are atoms for which no coordinates were assigned by the crystallographer, e.g . due to ambiguous electron density. Assuming there were no problems, s.gpf and s.dpf should be successfully produced.

• prepare-gpf+dpf

 
Usage
: prepare-gpf+dpf macro lig

Executes only steps 6. through 8.

• rem-lp

 
Usage
: rem-lp lig.pdbq
or
: rem-lp lig.mol2
Creates:
 lig.pdbq
or
: lig.mol2

This removes the lone-pairs (atom name = LP) added by some molecular modelling programs, such as SYBYL, and adds their partial charges on to that of the atom to which they were attached (SG in cysteines and SD in methionines). Otherwise, AutoDock treats lone-pairs as carbon atoms. (Note: if you need lone-pairs, you can force AutoGrid to calculate a grid map for "LP" atoms, using the atom code "L" in the "types" commands of AutoGrid and AutoDock).

• renumberatoms

 
Usage
: lig.pdb > lig2.pdb

• Used to renumber the atom IDs in the first column of the ATOM and HETATM records of a PDB file. Also updates the CONECT records appropriately.
• renumber-residues

 
Usage
: lig.pdb > lig.rnm

Used by prepare to renumber residues in the macromolecule contiguously. This step is needed prior to using protonate , which may fail if there are gaps in the residue numbers.

• resrange

 
Usage
: resrange lig.pdb

This is handy to summarise the range(s) of residues in a given protein PDB file.

• runtrj

 
Usage
: runtrj lig

Needs:
 lig.dpf
, lig.trj

Creates:
 lig.tcom
, lig.tlg
 and
 lig.tout

This creates an AutoDock command file, lig.tcom , which is then used to convert the trajectory written in state variables ( lig.trj ), into a trajectory written in cartesian coordinates. lig.trj is created by an earlier run of AutoDock , in which trjfrq was set to a non-zero value.

• stats

 
Usage
: stats columns.dat

This is a very useful, general awk program. Use it to calculate the minimum, maximum, mean and standard deviation for each column of numbers in an input file, here ` columns.dat '. Any alphanumeric columns will be ignored.