Commit 196e150f authored by Jacob Durrant's avatar Jacob Durrant

Added Open Babel warning.

parent 8cce02c4
......@@ -51,15 +51,15 @@ The program accepts the following parameters:
```
Note: It is best to use multiple neural networks to judge ligand binding by
consensus. Commandline parameters can be used to add neural-network files to
consensus. Command-line parameters can be used to add neural-network files to
the list of those that will be used. To add a single neural network to the
list, use the -network parameter to specify a single network file. To add
multiple networks to the list, create a directory containing only network
files and specify the path to that directory using the -networks_dir
parameter.
Note: Only pdbqt files of the receptor and ligand are accepted. Scripts to
convert from pdb to pdbqt are included in the [AutoDockTools
Note: Only PDBQT files of the receptor and ligand are accepted. Scripts to
convert from PDB to PDBQT are included in the [AutoDockTools
package](http://autodock.scripps.edu/resources/adt).
Examples:
......@@ -95,19 +95,21 @@ suited to your needs.
### REQUIREMENTS ###
Python3: A copy of the Python interpreter can be downloaded from
[http://www.python.org/getit/](http://www.python.org/getit/).
AutoDock Vina 1.1.2: NNScore 2.0 uses AutoDock Vina 1.1.2 to obtain some
information about the receptor-ligand complex. Note that previous versions of
AutoDock Vina are not suitble. AutoDock Vina 1.1.2 can be downloaded from
[http://vina.scripps.edu/download.html](http://vina.scripps.edu/download.html).
MGLTools: As receptor and ligand inputs, NNScore 2.0 accepts models in the
PDBQT format. Files in the more common PDB format can be converted to the
PDBQT format using scripts included in MGLTools (`prepare_receptor4.py` and
`prepare_ligand4.py`). MGLTools can be obtained from
[http://mgltools.scripps.edu/downloads](http://mgltools.scripps.edu/downloads).
* Python3: A copy of the Python interpreter can be downloaded from
[http://www.python.org/getit/](http://www.python.org/getit/).
* AutoDock Vina 1.1.2: NNScore 2.0 uses AutoDock Vina 1.1.2 to obtain some
information about the receptor-ligand complex. Note that previous versions
of AutoDock Vina are not suitable. AutoDock Vina 1.1.2 can be downloaded
from
[http://vina.scripps.edu/download.html](http://vina.scripps.edu/download.html).
* MGLTools: As receptor and ligand inputs, NNScore 2.0 accepts models in the
PDBQT format. Files in the more common PDB format can be converted to the
PDBQT format using scripts included in MGLTools (`prepare_receptor4.py` and
`prepare_ligand4.py`). MGLTools can be obtained from
[http://mgltools.scripps.edu/downloads](http://mgltools.scripps.edu/downloads).
**Be sure to use MGLTools to convert from PDB to PDBQT, not Open Babel.
These two programs do not assign the same partial atomic charges, and
NNScore was trained using MGLTools-assigned charges.**
### COMMAND-LINE PARAMETERS ###
......
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