[Dock-fans] Announcing: Release of DOCK 6.2

[Mysinger, Michael]

Dear Previous DOCK 6 Users,

If you already have an academic DOCK 6 license and you still have download slots available, then can just use your original download information to acquire DOCK 6.2. If you have used all your download slots, you will need to send an email to dock_license at dock.compbio.ucsf.edu requesting a refresh. 

If you have never applied for a academic DOCK 6 license, then you should use this link to apply: http://dock.compbio.ucsf.edu/Online_Licensing/index.htm

Cheers to the DOCK coders for the new release,
Michael Mysinger

-----Original Message-----
From: dock-fans-bounces at docking.org on behalf of Scott Brozell
Sent: Tue 3/4/2008 5:57 PM
To: dock-fans at docking.org
Subject: [Dock-fans] Announcing: Release of DOCK 6.2
 
Dear DOCK Users,

We are proud to announce the official release of DOCK version 6.2,
which includes several new features (see below for details).
Documentation and tutorials for this release can be found at
http://dock.compbio.ucsf.edu/DOCK_6/index.htm

If you would like to access the new version, apply for a new DOCK 6
license at http://dock.compbio.ucsf.edu/Online_Licensing/index.htm

Thank you for your continued interest in DOCK. We hope this software is
a useful part of your design efforts.

Sincerely,

The DOCK Team

Please visit us at the DOCK Web site.
http://dock.compbio.ucsf.edu

--- * ---

NEW IN DOCK 6.2

###Grid Reading Memory Efficiency###
   The various DOCK classes that handle grid reading and analysis have
been refactored.  As a direct result, grids are now only read once and
then accessed by various scoring functions, thus significantly reducing
the memory used when multiple grid-based scoring functions are called.

###Conformation Output Control###
   In version DOCK 6.1, we forced writing of all scored conformations.
We have since found that this option significantly increases the length
of the calculation and can take up inappropriate amounts of disk space for
large libraries.  Previously, the parameter num_scored_conformers_written
controlled both the number of conformations scored by the primary scoring
function, as well as the number of conformations written.  In the new
release, these two functions have been decoupled into two user parameters:
num_scored_conformers, which sets the number of conformations to be scored
by the primary scoring function, and write_conformations, which controls
whether these conformations will be written.  Similarly,
num_secondary_scored_conformers_written has been decoupled into
num_secondary_scored_conformers and write_secondary_conformations.
These changes provide users with greater control over conformation output.

###Continuous Score Distance Dependent Dielectric Control###
   The distance dependence of the dielectric factor in the
electrostatic term of the continuous score of DOCK can now be switched
off via input parameter cont_score_use_dist_dep_dielectric.

###Amber Score Improvements###
   The error reporting and robustness
of the Amber score preparation scripts have been improved.
If any step in the amberization fails fatally then termination is immediate.
Detection of parmchk "ATTN, needs revision" messages for missing force
field parameters and a recovery/override mechanism for the frcmod files
have been added.  The recovery process is described in the warning message
and involves creating a ligand_prefix.frcmod.revised file.
The override mechanism is the file parameters/leap/cmd/leaprc.dock.user
that is now sourced by every amberization script.
Automatic support for a simple treatment of metal ions based on Amber's
ff94 has been added: parameters/leap/cmd/leaprc.dock.ions.
A library that is automatically used has been started for common cofactors:
parameters/leap/cmd/leaprc.dock.cofactors.
Support for RNA receptors has been added.
The new script prepare_rna_amber.pl differs from prepare_amber.pl
only in that the former assumes that any nucleic acids are RNA
whereas the latter assumes DNA.
Minimization convergence criterion specification via input parameter
amber_score_minimization_rmsgrad has been added.  In verbose mode
Amber score now emits at every step (ntpr=1).
Skipping of inadequately prepped ligands via the input parameter
amber_score_abort_on_unprepped_ligand has been added.

###Sphere Selector###
   The total number of spheres is now unlimited, eliminating the previous
maximum of 100000 spheres.

###Miscellaneous###
   Incremental improvements in documentation, installation, and testing.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

DEPRECATED FEATURES

1.  For a variety of reasons still under active development,
amber_score cannot effectively be used as a secondary_score.
This function was temporarily deprecated in 6.1, and using input parameter
amber_score_secondary causes program termination.
The recommended protocol is to perform two DOCK runs with the second run
specifying amber_score as the primary_score.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

BUG FIXES

Some bug reports have not yet been processed, but
several important bugs have been fixed since the last release.

For DOCK:
   Ensure all cliques are examined as orients including the last one.
   Incorrect electrostatics with gbsa_hawkins_score_cont_vdw_and_es = yes.
   Incorrect communication of the Amber score ligand identifier.
   Memory leak in Amber score due to absent freeing of nab molecules.
   Incorrect documenting and handling of the charge options in amberize_ligand.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

INPUT PARAMETER CHANGES

Added:
   amber_score_minimization_rmsgrad                             0.01
   amber_score_abort_on_unprepped_ligand                        yes
   cont_score_use_dist_dep_dielectric                           yes
   num_scored_conformers                                        1
   num_secondary_scored_conformers                              1
   write_secondary_conformations                                yes

Removed:
   num_scored_conformers_written                                1
   num_secondary_scored_conformers_written                      1



_______________________________________________
Dock-fans mailing list
Dock-fans at docking.org
http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans