Hi Christine,
You can split outputs by this way (vina site) :
Separate models
All predicted binding modes, including the positions of the
flexible side chains are placed into one multimodel PDBQT file
specified by the "out" parameter or chosen by default, based on
the ligand file name. If needed, this file can be split
into individual models using a separate program called
"vina_split", included in the distribution.
Le 25/02/2013 23:46, Harman, Christine a écrit :
[log in to unmask]"
type="cite">
Hi All,
I am sure that some of you have used AutoDock Vina so I
thought I would give it a go and ask two questions. I
performed a round of docking and obtained an output file
containing 9 different models. The affinity (kcal/mol)
ranged from -4.5 to -3.0. My
first question is what is considered high binding affinity
i.e. what range is considered high affinity, moderate
affinity etc. My second question is about the output file.
The output file is in pdbqt format and can be viewed in
Pymol just fine, but the problem
is that I cannot separate out the individual orientations of
the output file. I want to change the format to pdb so that
I can change the depiction of the models in PyMol, but PyMol
treats the file as one file and will not allow me to read
out the models as
separate pdb files. Does anybody know how to separate out
the different models contained in one output file provided
by AutoDock Vina. Thanks for any advice.
Take care,
Christine