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 :
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