[med-svn] r1484 - trunk/packages/autodocksuite/trunk/debian
smoe-guest at alioth.debian.org
smoe-guest at alioth.debian.org
Fri Feb 29 09:53:24 UTC 2008
Author: smoe-guest
Date: 2008-02-29 09:53:23 +0000 (Fri, 29 Feb 2008)
New Revision: 1484
Modified:
trunk/packages/autodocksuite/trunk/debian/README.Debian
trunk/packages/autodocksuite/trunk/debian/autodock4.1
trunk/packages/autodocksuite/trunk/debian/autogrid4.1
trunk/packages/autodocksuite/trunk/debian/control
trunk/packages/autodocksuite/trunk/debian/copyright
Log:
Incorporating feedback from upstream.
Some further improvements on wording here and there.
Modified: trunk/packages/autodocksuite/trunk/debian/README.Debian
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/README.Debian 2008-02-28 20:44:02 UTC (rev 1483)
+++ trunk/packages/autodocksuite/trunk/debian/README.Debian 2008-02-29 09:53:23 UTC (rev 1484)
@@ -2,11 +2,11 @@
------------------------
AutoDock is a prime representative of the programs addressing the
-simulation of the docking of fairly small chemical ligands to
-rather big protein receptors. Earlier versions had all flexibility
-in the ligands while the protein was kept rather ridgid. This latest
-version 4 also allows for a flexibility of selected sidechains of surface
-residues, i.e., takes the rotamers into account.
+simulation of the docking of fairly small chemical ligands to rather big
+protein receptors. Earlier versions had all flexibility in the ligands
+while the protein was kept rather ridgid. This latest version 4 also
+allows for a flexibility of selected sidechains of surface residues,
+i.e., takes the rotamers into account.
This package was not yet tested in practice. Please give respective
feedback. You may find other spots where to help with packaging. The
@@ -21,9 +21,10 @@
Debian-Med underneath the packages/mgltools folder. More information is
in the README at the same location.
-Dr Garrett Morris of the upstream developers is very much looking forward to
-see AutoDock being distributed with Debian. The Scripps Institute asks for
-registrations prior to the download of the tarball or the binaries at this URL
+Dr Garrett Morris of the upstream developers is very much looking forward
+to see AutoDock being distributed with Debian. The Scripps Institute asks
+for registrations prior to the download of the tarball or the binaries
+at this URL
http://autodock.scripps.edu/downloads/autodock-registration
@@ -34,7 +35,9 @@
popularity-contest. This counts the installations and may thus further
help upstream to further develop their software.
-Thanks for improving the AutoDock/-Grid packaging for Debian go to David
+Dr Morris kindly proofread the copyright notice and the autogrid4.1 man
+page. This was much appreciated and I thank him for this. Thanks for
+improving the AutoDock/-Grid packaging for Debian also go to David
Paleino and the Debian-Med community at large.
Steffen
Modified: trunk/packages/autodocksuite/trunk/debian/autodock4.1
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/autodock4.1 2008-02-28 20:44:02 UTC (rev 1483)
+++ trunk/packages/autodocksuite/trunk/debian/autodock4.1 2008-02-29 09:53:23 UTC (rev 1484)
@@ -19,9 +19,14 @@
autodock \- docking of chemical ligands to protein receptors
.SH SYNOPSIS
.B autodock4
-.RI [ options ] " files" ...
+.RI [ options ]
.SH DESCRIPTION
-The maintainer of the Debian package does not yet feel sufficiently competent to prepare this man page. Please help.
+AutoDock perfoms the automated docking of chemical compounds to proteins, i.e. it
+predicts how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
+
+The AutoDockSuite consists of two main programs of which AutoDock performs the
+docking of the ligand to a set of grids describing the target protein and
+AutoGrid pre-calculates these grids.
.PP
.\" TeX users may be more comfortable with the \fB<whatever>\fP and
.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
@@ -35,27 +40,27 @@
.RI log_filename
.TP
.B \-o
-(Use old PDBQ format, charge q in columns 55-61)
+Use old PDBQ format, charge q in columns 55-61
.TP
.B \-k
-(Keep original residue numbers)
+Keep original residue numbers
.TP
.B \-i
-(Ignore header-checking)
+Ignore header-checking
.TP
.B \-t
-(Parse the PDBQ file to check torsions, then stop.)
+Parse the PDBQ file to check torsions, then stop.
.TP
.B \-c <
.RI command_file
-(Command mode, by file)
+Command mode, by file
.TP
.B \-c |
.RI control_program
-(Command mode, by control_program)
+Command mode, by control_program
.SH EXAMPLE
-On Debian, the directory /usr/share/doc/autodock offers examples to run. Change to that directory and unpack (as root) the gzipped map files, then execute autodock as shown below:
+On Debian, the directory /usr/share/doc/autodock offers examples to run. Change to that directory and unpack (as root) the gzipped map files, then execute AutoDock as shown below:
.br
gunzip *.map.gz
.br
@@ -68,6 +73,8 @@
.BR runAdt (1).
.br
http://autodock.scripps.edu
+.br
+http://autodock.scripps.edu/faqs-help/faq/what-is-the-command-line-to-start-autodock-4
.SH LICENSE
This software is made available under the terms of the GNU Public
License version 2 or later. This implies that this software may be
Modified: trunk/packages/autodocksuite/trunk/debian/autogrid4.1
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/autogrid4.1 2008-02-28 20:44:02 UTC (rev 1483)
+++ trunk/packages/autodocksuite/trunk/debian/autogrid4.1 2008-02-29 09:53:23 UTC (rev 1484)
@@ -13,21 +13,36 @@
.\" .sp <n> insert n+1 empty lines
.\" for manpage-specific macros, see man(7)
.SH NAME
-autogrid \- preparing protein and ligand for autodock analysis
+autogrid \- preparing protein and ligand for AutoDock analysis
.SH SYNOPSIS
.B autogrid4
.RI [ options ]
-p
.RI gridparameterfile
.SH DESCRIPTION
-.B autogrid4
-prepares a 3D grid representation of the non-binding forces that a
-point charge will experience at any location around the protein or
-in its binding pocket. The grid is calculated for all the atom types
-that are known to autodock. The input to
-.RI autogrid4
+.B AutoGrid
+prepares a 3D grid representation of the non-covalent interaction
+energies that various user-specified ligand atom types will experience
+around a user-specified target macromolecule. In addition, the
+electrostatic potential and desolvation free energy grid maps may also
+be calculated. The grid maps are stored in plain text files with the
+extension '.map' and are required by AutoDock 4 to perform dockings.
+AutoGrid also outputs a '.xyz' file which describes the spatial
+extents of the grid box, and an AVS field '.fld' file which describes
+the consistent set of atomic affinity grid maps that were calculated
+together for a given target macromolecule. Note: it is necessary
+to compute grid maps for all the atom types in the ligand or set of
+ligands that will be docked, as well as an electrostatic potential
+grid map and a desolvation free energy map. For example, if a ligand
+has an aliphatic carbon and a hydrogen-bond-accepting oxygen atom,
+it would be necessary to compute both a 'C' map and an 'OA' map. See
+http://autodock.scripps.edu/faqs-help/faq/where-do-i-set-the-autodock-4-force-field-parameters
+for more information about AutoDock 4 atom types.
+
+The input to
+.RI AutoGrid
is best prepared with the program suite
-.RI autodocktools.
+.RI AutoDockTools.
There is no way to run
.RI autodock4
without a grid.
@@ -37,10 +52,6 @@
.\" respectively.
.ad l
.SH OPTIONS
-.TP
-\fB\-o\fR
-Use old PDBq format (q in columns 55-61)
-.TP
.B \-o
Use old PDBq format (q in columns 55-61)
.TP
@@ -71,7 +82,7 @@
$ autogrid4 -p $D/hsg1_no_receptor_types.gpf -l hsg1_no_receptor_types.glg
.ad b
.TP
-This command prepares grid files for each of the AutoDock atom types (hsg1_sm.A.map, hsg1_sm.C.map, hsg1_sm.d.map, hsg1_sm.e.map, hsg1_sm.HD.map, hsg1_sm.NA.map, hsg1_sm.N.map, hsg1_sm.OA.map), the AVS field file (hsg1_sm.maps.fld) and hsg1_sm.maps.xyz. For performing the computation, autodock is executed, though it demands a separate parameter .dpf file that assignes these newly created files to the docking process and allows the setting of further parameters.
+This command prepares grid map files for each of the AutoDock atom types specified in the grid parameter file (in this case: hsg1_sm.A.map, hsg1_sm.C.map, hsg1_sm.d.map, hsg1_sm.e.map, hsg1_sm.HD.map, hsg1_sm.NA.map, hsg1_sm.N.map, hsg1_sm.OA.map), the AVS field file (hsg1_sm.maps.fld) and hsg1_sm.maps.xyz. To perform the cocking calculation, AutoDock should be executed, though it demands a separate docking parameter file (with extension .dpf). The 'DPF' refers to the grid map files that are necessary to the docking and allows the setting of other important parameters, such as the search method and how many dockings to perform.
.SH SEE ALSO
.BR autodock (1),
@@ -85,10 +96,11 @@
the future development of the AutoDockSuite if you register yourself
at http://autodock.scripps.edu/downloads.
.SH AUTHOR
-The most prominent author of the version 4 of autodock is G. Morris
+The most prominent author of the version 4 of AutoDock is G. Morris
<garrett at scripps.edu>. See the AUTHORS file in /usr/share/doc/autogrid
for details.
.PP
-This manual page was written by Steffen Moeller <moeller at debian.org>,
-for the Debian project (but may be used by others and is hopefully
-adopted by the upstream developers).
+This manual page was written by Steffen Moeller <moeller at debian.org>
+and much revised by upstream author Garrett Morris.
+It was prepared for the Debian project but may be used by others and
+is hopefully adopted by the upstream developers.
Modified: trunk/packages/autodocksuite/trunk/debian/control
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/control 2008-02-28 20:44:02 UTC (rev 1483)
+++ trunk/packages/autodocksuite/trunk/debian/control 2008-02-29 09:53:23 UTC (rev 1484)
@@ -15,9 +15,12 @@
Recommends: autogrid
Suggests: popularity-contest
Description: analysis of ligand binding to protein structure
- The AutoDockSuite addresses the molecular analysis of the docking of
- a smaller chemical compounds to their receptors of known three-dimensional
- structure.
+ AutoDock is a prime representative of the programs addressing the
+ simulation of the docking of fairly small chemical ligands to rather big
+ protein receptors. Earlier versions had all flexibility in the ligands
+ while the protein was kept rather ridgid. This latest version 4 also
+ allows for a flexibility of selected sidechains of surface residues,
+ i.e., takes the rotamers into account.
.
The AutoDock program performs the docking of the ligand to a set of
grids describing the target protein. AutoGrid pre-calculates these grids.
Modified: trunk/packages/autodocksuite/trunk/debian/copyright
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/copyright 2008-02-28 20:44:02 UTC (rev 1483)
+++ trunk/packages/autodocksuite/trunk/debian/copyright 2008-02-29 09:53:23 UTC (rev 1484)
@@ -5,34 +5,38 @@
Upstream Authors:
- Peter Reilly
- Max Chang
- Rik Belew
+ Primary:
+
+ Garrett M. Morris <garrett at scripps.edu>
+ David S. Goodsell <goodsell at scripps.edu>
Scott Halliday
- Scott Kurowski <scott at scottkurowski.com>
- Bill Hart <wehart at sandia.gov>
- Garrett M. Morris <garrett at scripps.edu>,
- David S. Goodsell <goodsell at scripps.edu>
Ruth Huey <rhuey at scripps.edu>
+ William E. Hart <wehart at sandia.gov>
+ Max Chang <mchang at ucsd.edu>
Richard K. Belew <rik at cogsci@ucsd.edu>
- Arthur J. Olson
+ Arthur J. Olson <olson at scripps.edu>
+ Contributing:
+
+ Peter Reilly <reilly at iastate.edu>
+ Scott Kurowski <scott at scottkurowski.com>
+
Copyright:
- Copyright (C) 1989-2007
- Peter Reilly
- Max Chang
- Rik Belew
+ Copyright (C) 1989-2008, All Rights Reserved.
+ Garrett M. Morris <garrett at scripps.edu>
+ David S. Goodsell <goodsell at scripps.edu>
Scott Halliday
- Scott Kurowski <scott at scottkurowski.com>
- Bill Hart <wehart at sandia.gov>
- Garrett M. Morris <garrett at scripps.edu>
- David S. Goodsell <goodsell at scripps.edu>
Ruth Huey <rhuey at scripps.edu>
+ William E. Hart <wehart at sandia.gov>
+ Max Chang <mchang at ucsd.edu>
Richard K. Belew <rik at cogsci@ucsd.edu>
- Arthur J. Olson
- and The Scripps Research Institute <autodock at scripps.edu>
+ Arthur J. Olson <olson at scripps.edu>
+ Peter Reilly <reilly at iastate.edu>
+ Scott Kurowski <scott at scottkurowski.com>
+ and The Scripps Research Institute
+
License:
AutoDock is a Trade Mark of The Scripps Research Institute.
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