1.1.1 -> 1.1.2:
* Bug fix: the affinities reported with flexible side chains were
sometimes incorrect. (This problem had no effect on the predicted
binding modes or their relative ranking, or on rigid receptor
* Bug fix: the individual term values, before weighting, reported
only with “score_only”, were often wrong. (This problem
had no effect on the predicted binding modes or affinities)
* The predicted binding modes are made less redundant by requiring
that no two reported modes differ by less than 1 Angstrom RMSD(U.B.),
counting all movable heavy atoms, including those in the side chains.
Previously, Vina avoided this kind of redundancy during the actual
docking, but made no such guarantee w.r.t. the output because
of the subsequent refinement stage that could move different binding
* Bug fix: in some very unusual cases, numerical rounding errors would
accumulate, leading, internally, to a distorted ligand structure.
The self-checks in Vina would catch this and make the program quit
rather than write invalid output. This numerical error accumulation
is believed to have been fixed in this update
* A warning is added when the search space is greater than
27000 Angstrom^3 in volume, as confusing Angstroms with
“grid points” is a frequent user error
1.1.0 -> 1.1.1:
* Source code released
* License changed to Apache
* Extensive code clean-up that however should not have any effect
on the end users
* Unix binary packages changed to simple archives
1.0.3 -> 1.1.0:
* Added “advanced options” intended to be primarily used by people
interested in methods development.
These should allow scoring without minimization; performing
local optimization only; randomizing the input with no search
(this is useful for testing docking software); changing the
weights from their default values; displaying the individual
contributions to the intermolecular score, before weighting
(these are shown with “–score_only”)
1.0.2 -> 1.0.3:
* Mac OS X 10.6 (Snow Leopard) support added
* A bug related to (very rarely) not finding any modes when the
“num_modes” setting is low (e.g. 1) has been fixed.
1.0.1 -> 1.0.2:
* Fixed a bug that excluded conformations in which only a hydrogen atom was
outside the search space.
1.0 -> 1.0.1:
* When the search space is too small or misplaced, so that the ligand and
flexible side chain conformations can not be found within it, Vina will
no longer produce any “binding modes” and print a warning instead
* Minor improvements in user-friendliness of the error messages.
1.0 Beta 04 -> 1.0:
* Support for earlier versions of Linux added, such as Debian 4.0
* Friendlier and more specific error messages for PDBQT syntax errors
* “all” parameter is now called “out” and is always enabled. Individual
binding modes are no longer written separately. If needed, the multimodel
output can be split into individual models using a separate program
called “vina_split”, included in the distribution
* The default “num_modes” value changed to 9.