[Dock-fans] Announcing: Release of DOCK 6.3

Scott Brozell sbrozell at rci.rutgers.edu
Fri Jul 24 19:33:23 PDT 2009

Dear DOCK Users,

We are proud to announce the official release of DOCK version 6.3,
which includes several new features (see below for details).
Documentation and tutorials for this release can be found at

If you already have an academic DOCK 6 license and you still have
download slots available, then you can use your original download
information to acquire DOCK 6.3. If you have used all your download
slots then request a refresh in an email to
dock_license at dock.compbio.ucsf.edu.

If you have never applied for an academic DOCK 6 license then apply at

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


The DOCK Team

Please visit us at the DOCK Web site.

--- * ---

DOCK 6.3

This is a release of the version applied in the DOCK6 paper [1].
Recent improvements to the sampling implementation and corrections to 
prevent steric clashes that have been mentioned on the Dock-fans list
[2] are not incorporated here; they will appear in the next version
which is expected to be released soon.


###Amber Score Improvements###
   The distance movable region can be applied to receptors that include
explicit waters.  This is useful for RNA-small molecule complexes [1],
and it required changing the ligand position in the complex from the
last strand to the first strand; this implementation detail has resulted
in input parameter changes for the nab_atom_expression movable region.
The preparation of RNA receptors can neutralize to a total charge of zero
and can solvate with water.  These are done via LEaP, and its charge
tolerance has been increased from 0.0001 (as in Amber10) to 0.001 to
avoid excessive instances of left over charges of plus or minus one.
An option to use the existing ligand charges has been added to both
prepare_amber.pl and prepare_rna_amber.pl. This automates efficient
rescoring with multiple scores; note that Amber Score is more sensitive to
charges than other DOCK Scores; so the existing charges should be good ones.
The error reporting and robustness of the Amber score preparation scripts
have been improved; a final fail check (for a nonzero sized prmtop file)
has been added.  The amberize output file names now use the complete ligand
identifiers to avoid overwriting in batch processing of multiple multi-ligand
calculations.  The ions library, leaprc.dock.ions, has grown modestly.

###PB/SA Score Improvements###
   Updated to OpenEye Toolkits version 1.7.0.  In particular, DOCK uses
the APIs as in OEChem TK 1.7.0 and Zap TK 2.1.1.

###Input File Processing###
   Unused dock6 input name/value pairs are no longer silently ignored;
now a warning is emitted.

   64 bit platforms are now fully supported although the test suite
temporarily still contains reference outputs from a 32 bit platform.
Several configuration files have been added; thanks to Francesco Pietra
for testing the ones for Intel compilers.  SGI platforms are no longer
supported.  Ubuntu Linux is supported; recent GNU compilers emit lots
of warnings when building DOCK that should be ignored.
g77 is still the default Fortran compiler. But gfortran comes with any not
too old GNU compiler installation; hand edit install/config.h to use it.
parameters/prot.table.ambcrg.pdb3H has been created in an effort to begin
supporting PDB version 3 naming.



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.



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

   Incorrect Amber score distance movable residue selection.
This bug was only exercised when a strand had no residues within
the distance cutoff; in that case the whole strand instead of none
of the strand was selected by the generated NAB atom expression.

   Flexible ligand pruning without clustering ignored input parameter
pruning_conformer_score_cutoff increasing the number of conformations.

   Incorrect PB/SA score PB component energy units.

   For chemical matching the centers index list was being resized
to the sphere list size instead of the centers list size.

   Zou GB/SA Score reading of the GB and SA grids on 64 bit platforms.

   Missing C header file inclusions.

For grid-convert:
   Fatal termination with contact_score = yes.

For nchemgrid_GB:
   Zou GB/SA Score writing of the GB grids on 64 bit platforms.

For nchemgrid_SA:
   Zou GB/SA Score writing of the SA grids on 64 bit platforms.



   amber_score_receptor_movable_atom_expr                       "::"
   amber_score_complex_movable_atom_expr                        "::"

   amber_score_movable_atom_expression                          "::"



   The label for RMSDs in structural output files has changed from 
'########## RMSD' to '#HEAVY ATM RMSD'.

For nchemgrid_GB:
   The .rec file has changed from binary to textual representation.

For nchemgrid_SA:
   The .sas file has changed from binary to textual representation.



1. "DOCK 6: Combining Techniques to Model RNA-Small Molecule Complexes,"
P. T. Lang, S. R. Brozell, S. Mukherjee, E. F. Pettersen, E. C. Meng, V.
Thomas, R. Rizzo, D. A. Case, T. L. James, and I. D. Kuntz, RNA, Vol. 15,
1219-1230 (2009). 

2. http://blur.compbio.ucsf.edu/pipermail/dock-fans/2009-May/002058.html

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