Your message dated Tue, 19 Feb 2013 11:00:32 +0100
with message-id <[email protected]>
and subject line autodocksuite 4.2.5 just uploaded to experimental
has caused the Debian Bug report #697819,
regarding autodocksuite: New upstream version 4.2.5.1
to be marked as done.
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--
697819: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=697819
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: autodock
Version: 4.2.3-1
Severity: wishlist
Tags: upstream
AutoDock 4.2.5.1 Release Notes:
http://autodock.scripps.edu/downloads/autodock-4-2-release-notes
=============================================================================
AutoDock Release Notes
Release 4.2.5.1 (December 2012)
=============================================================================
The changes since the 4.2.5 release (11/02/2012):
#bug fix
4.2.5 incorrectly calculated part of the intermolecular desolvation
energy term; 4.2.5.1 corrects this. All 4.2.5 users should upgrade
to 4.2.5.1 and re-do any runs.
=============================================================================
AutoDock Release Notes
Release 4.2.5 (November 12 2012)
=============================================================================
Please note that the previous general release was 4.2.3, 29 January 2010.
The 4.2.4 release (7 July 2010) was a specialized release for
"Fight Aids at Home" and other IBM World Community Grid projects.
Supported computer platforms in 4.2.5:
Linux2 on Intel x86 remains supported, as does Solaris 8 on SPARC.
Supported Macintosh platforms are OS X 10.4-10.5 (Tiger and Leopard) on
Intel x86 and PowerPC, and OS X 10.6-10.8 (Snow Leopard, Lion, and
Mountain Lion) on Intel x86. The executable binaries for Windows on
Intel x86 have been built on Windows 5 (XP) and have been tested on Windows 6
and Windows 7. Windows users no longer need to install the CygWin environment,
but they may if they like.
The changes since the 4.2.3 release (1/29/2010):
#new features
-: new support for specifying output verbosity ranging from low (-2) up to high
(8)
with symbolic settings for "outlev" defined in constants.h and used in
main.cc
-: new automatic calculation of 'about' as the center of the ligand root group
-: new WIN32 MinGW portability - replacements for times() and getrusage()
-: new desolvation term separate from vdW+Hbond term in epdb
"Per-atom Intermolecular Energy Analysis" table
-: now intelec is on by default; off if "intelec off" in DPF
-: Almost all AutoDock defaults now match defaults supplied by ADT, simplifying
PDF files
#code inspection and internal interface self-documentation
-: We thank Steffen Moeller ([email protected]) for his enthusiastic
and expert detailed inspection of all function and method calls,
in particular identifying "constant" arguments and verifying
data type compatibiliy.
#improvements
-: improved detailed output of Intermolecular Energy Analysis
-: increased MAX_RUNS from 256 to 2000
-: improved error detection and termination:
replaced exit() by EXIT_SUCCESS/EXIT_FAILURE(win32) or stop(msg)
-: increased precision of energy table
-: implemented EnergyComponent structures
-: integrated call_gs into call_glss
-: improved input checking with ga_run/gals_run
[Added checks to "ga_run/gals_run" for missing "set_ga" and missing "set_psw1"
errors]
-: simplified logic so more of the FATAL errors are simply handed to "stop()"
-: now set random number seeds at beginning of simanneal execution; output
reduced
-: new compile-time option to print energy terms for each atom [for debugging]
-: AutoDock intramolecular energy smoothing now matches that in AutoGrid
-: Consolidated the "side effects" of trilinterp that record per-atom energy
components
and total energy components into two sets of "EnergyComponent" structures
instead
of two Real arrays and two pointers to Real.
-: developed substitutes for WIN32 MinGW "times()" and "getpid()"
-: modified mkTorTree.cc to fill in the root atom information
-: Changed 'tlist' declaration to allow space for root atoms at end
#bug fixes
-: corrected energy breakdown report when using flexible residues
-: desolvation energy term is included even for distant pairs (r>nbc)
-: corrected eintcal side effects of "outlev" setting
-: removed support for unused DPF tokens
#autogrid
AutoGrid 4.2.5 has no functional changes from AutoGrid 4.2.3.
The only significant code changes were those required for porting to Windows.o
We added 'copyfilesfromAD', a maintenance script that copies key shared source
files
from AutoDock to AutoGrid.
-- System Information:
Debian Release: 6.0.6
APT prefers stable-updates
APT policy: (500, 'stable-updates'), (500, 'proposed-updates'), (500,
'stable')
Architecture: amd64 (x86_64)
Kernel: Linux 3.2.0-0.bpo.4-amd64 (SMP w/4 CPU cores)
Locale: LANG=it_IT.UTF-8, LC_CTYPE=it_IT.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Versions of packages autodock depends on:
ii libc6 2.11.3-4 Embedded GNU C Library: Shared lib
ii libgcc1 1:4.4.5-8 GCC support library
ii libstdc++6 4.4.5-8 The GNU Standard C++ Library v3
autodock recommends no packages.
Versions of packages autodock suggests:
pn autodocktools <none> (no description available)
pn autogrid <none> (no description available)
-- no debconf information
--- End Message ---
--- Begin Message ---
Hello,
Thank you for pointing us to the update. You may now retrieve it from the
experimental section of Debian. Debian is in a deep freeze for a while and will
ship with the now outdated version, sadly. You find an immediate download here
http://packages.debian.org/search?keywords=autodock
With many thanks to Thorsten for the update
Steffen
--- End Message ---
