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This page will grow and become more
useful over time. Check here before you bug, niggle, taunt,
tease, fluster, tickle or hassle a human. Please... : )
- Does AutoDock run on Mac OS X?
- Does AutoDock run on Linux?
- I used "get-dockings" to extract the docked conformations. Where is the macromolecule?
- Do you have parameters for halogens (F, Cl, Br & I)?
- I would like to model a heme in my protein. How do I treat the tetrapyrrole nitrogen atoms and the iron atom?
- How do I prepare my macromolecule and ligand for docking with AutoDock?
- I can't find the script "q.amber" which assigns partial charges according to the AMBER force field. Where is it?
- When running some scripts, I get the error message "/usr/bin/nawk: arg list too long". What's wrong?
Since Mac OS X ("oh-ess-ten") is built on Darwin, the Open Source FreeBSD-based operating system, it was quite easy to port to this OS. You will find executables for AutoGrid and AutoDock in "dist305/bin/apple.MacOSX_10.1".
Note that you need to run the "Terminal" application to run AutoDock. AutoDock runs just like on any other UNIX system, from the command line. We are working on a port of our GUI, AutoDockTools, to Mac OS X. Currently, our progress is stalled because there is a bug in an open source component called "Togl" which we have reported to its authors, but there has been no response as yet.
Remember, to compile on Mac OS X, you need to install the "Developer Tools" which comes included with the Mac OS X CD-ROMs. If you do not have this disc, you can become an Online member of the Apple Developer Connection (ADC) for free, and download the Developer Tools, again for free. Hopefully you have a fast connection to the internet, because the December 2001 Mac OS X 10.1 Dev Tools are about 220 MB!
You will find the correct compiler options in the Makefiles - just look for the comments with "MacOS X" in them. These options are very similar to the Linux options.
Also, like Linux, you need to add "limit stacksize unlimited" to your ".cshrc", ".tcshrc", or other similar shell-run commands file.
Pierre Scotney has written a HOWTO on compiling AutoDock 3.0 under RedHat 6.0 GNU Linux, and is available at his web site. Remember that Linux sets a limit to the stacksize of 8MB by default. This is too small for AutoDock (and other programs) and causes a "segmentation fault" to occur immediately after reading in a ligand with the "move" command. The solution is to add this line to your ".cshrc", ".bashrc" or ".tcshrc" file, whichever is appropriate for your default shell:
limit stacksize unlimited
Then make sure you source your ".{c,ba,tc}shrc" file before trying to run "autodock3".
After you extract the docked conformations from the AutoDock log file using get-dockings, you obtain a PDB formatted file that contains the docked conformations of the ligand. These are sorted in order of increasing energy, and in accordance with the conformational clustering. This PDB file puts each docked conformation in between MODEL and ENDMDL records. This file does not contain the macromolecule coordinates which you docked to. Don't Panic! These are still in the original PDBQS file you used to generate the AutoGrid maps. In other words, the output docked coordinates of the ligand are written in the same reference frame as the original macromolecule PDBQS.
To view the dockings in relation to the macromolecule, in InsightII 2000, for example, read in the PDB file of MODELs first (with "Keep all frames" turned on). Then read in the macromolecule PDBQS file using the first docked conformation as the "Reference" structure. You can read in the PDBQS file as a PDB formatted file (it works in InsightII, except you do not see PDBQS files in the file browser: you must type in the PDBQS file name yourself.) You should now see the macromolecule and the docked conformations together.
Alternatively, you can add the macromolecule and the docked conformations together into one PDB file that contains everything. At the UNIX prompt, type this:
% get-dockings mydocking.dlg
% pdbqtopdb mymacromolecule.pdbqs
>> mydocking.dlg.pdb
This will append the macromolecule (in PDB format) to the stacked MODELs in the "mydocking.dlg.pdb" file, so you can now read in this file and you should see everything together.
You should take a look at the Parameters
page for the actual values of the non-bond parameters for halogens. Remember
that AutoGrid and AutoDock use a very simplistic way of detecting atom
types: they look at the first letter of each atom name in the PDBQ file.
This means you must edit the first letter of certain atom types:
| Element
name |
IUPAC
symbol |
AutoDock
single-letter code |
| Fluorine |
|
|
| Chlorine |
|
|
| Bromine |
|
|
| Iodine |
|
|
AutoGrid calculates a protein grid map for each of the atom types in your ligand. So if you were docking camphor to cytochrome P-450cam from Pseudomonas putida (PDB code 2cpp), you would need a C map, an O map and an electrostatic potential map. If you were using the untied-atom, or polar-hydrogen-only model, you would not need a map for non-polar H.
After preparing the macromolecule and ligand, and before calculating the grid maps, you must edit the atom names in the macromolecule PDBQS file. AutoGrid internally expects the macromolecule to have up to 7 different atom types. The 1-letter atom type-codes for these 7 are defined in the string ATOMTYPE, which is defined in "autogrid.h" on the line:
#define ATOMTYPE "CNOSHXM"
So type number 6 is `X' and 7 is `M'. These codes, `X' and `M', can be used for anything, but `M' is usually used for metals. Each of the seven-line `nbp_r_eps' blocks in the grid parameter file (GPF) correspond to macromolecule atom type codes. Make sure you have the latest version of "gpf3gen.awk", 3.0.4.
So you can model the non-hydrogen bonding
tetrapyrrole nitrogens by changing the first character of their atom names
from `N' to `X', in the macromolecule PDBQS file. Similarly, change
the first letter of the iron atom from `F' to `M'. Then on the 6th and
7th lines of the parameter blocks, change the r and epsilon
values to the appropriate values for the new atom types and change the
exponents from 12-10 to 12-6. (If the exponents are 12 and 10, AutoGrid
will assume this is a hydrogen bonding potential, and will use directional
potentials.) Here is the GPF:
| -
|
receptor 2cpp_nN.pdbqs #macromolecule gridfld 2cpp_nN.maps.fld #grid_data_file npts 60 60 60 #num.grid points in xyz spacing .375 #spacing (Angstroms) gridcenter 46.508 44.528 14.647 #xyz-coordinates or "auto" types CO #atom type names smooth 0.500 #store minimum energy within radius (Angstroms) map 2cpp_nN.C.map #filename of grid map <-- Ligand-Carbon Parameters nbp_r_eps 4.00 0.0222750 12 6 #C-C lj nbp_r_eps 3.75 0.0230026 12 6 #C-N lj nbp_r_eps 3.60 0.0257202 12 6 #C-O lj nbp_r_eps 4.00 0.0257202 12 6 #C-S lj nbp_r_eps 3.00 0.0081378 12 6 #C-H lj nbp_r_eps 3.75 0.0230026 12 6 #C-X lj <-- Change 6th line to model C-X lj nbp_r_eps 4.00 0.0222750 12 6 #C-M lj <-- and change the 7th line to model C-M lj sol_par 12.77 0.6844 #C atomic fragmental volume, solvation param. constant 0.000 #C grid map constant energy map 2cpp_nN.O.map #filename of grid map <-- Ligand-Oxygen parameters nbp_r_eps 3.60 0.0257202 12 6 #O-C lj nbp_r_eps 3.35 0.0265667 12 6 #O-N lj nbp_r_eps 2.65 0.0297000 12 6 #O-O lj 3.20 nbp_r_eps 3.60 0.0297000 12 6 #O-S lj nbp_r_eps 1.71 0.3280000 12 10 #O-H hb 1.90 nbp_r_eps 3.35 0.0265667 12 6 #O-X lj <-- Likewise, change 6th line to model O-X lj nbp_r_eps 3.60 0.0257202 12 6 #O-M lj <-- and 7th to model O-M lj sol_par 0.00 0.0000 #O atomic fragmental volume, solvation param. constant 0.236 #O grid map constant energy| elecmap 2cpp_nN.e.map #electrostatic potential map dielectric -0.1146 #<0,distance-dep.diel; >0,constant #fmap 2cpp_nN.f.map #floating grid |
- |
If you have SYBYL, you can look at this page, which describes how to use SYBYL, the commercial molecular modelling package from Tripos, in addition to some Unix utilities we've written, to help get your input files set up for use in AutoGrid and AutoDock. You can download these scripts freely.
If you don't have SYBYL, you can download the free GUI we have developed here at Scripps. It is called "AutoDockTools" and you can find out how to obtain it by going to the "Useful Tools" page.
You can download the "q.amber"
script here. This script has partial charges for all atom models,
including non-polar hydrogens. Remember to give the saved file the name
"q.amber", and executable permission, "chmod +x q.amber".
Also, if you need the Kollman united atom
charges, the "q.kollua"
script can be downloaded here.
This is because your OS cannot handle the very long nawk (or awk or gawk) program given to the shell, /bin/sh. Some OS's can handle this, but if you get this error, you should modify the script so that it calls a second file that just contains the awk program, and no /bin/sh line at the top. For example, if you get this error with gpf3gen, then download these two files, "gpf3gen" and "gpf3gen.awk", and give them both executable permission. At the Unix prompt, type:
% chmod +x gpf3gen gpf3gen.awkRename the original "gpf3gen" to "gpf3gen.original", and then move both these files to the same directory as the original "gpf3gen", wherever you keep your AutoDock utility scripts. Make sure you set your environment variable $AUTODOCK_UTI to point to this directory. You may have to type "rehash" at the Unix prompt in order for these changes to be recognized by your current shell.
[AD3, 19991109.1750. 19991109.1835]
| References | Versions | Obtaining | Movies | Documentation | Examples | Parameters | FAQ | Useful Tools | Work in Progress |