ADL: Alternative to MGLTools prepare_ligand4.py

Price, Gareth Gareth.Price at warwick.ac.uk
Tue Jul 23 14:46:10 PDT 2013


Dear all,

I am developing a small suite of python applications, one of which uses AutoDock Vina.

Currently, to prepare the PDBQT for screening, I am using  prepare_ligand4.py, which uses the pythonsh binary, both provided by the MGLTools package.

I am wanting to move the application to a cluster where it may not be possible to either a) access/run the pythonsh binary or b) run the prepare_ligand4.py program in an environment which means that it will work properly.

Thus, is there an alternative to prepare_ligand4.py? I am aware that it is assigning partial charges and atom types - is there a way to do this without the MGLTools dependency?

Many thanks,
Gareth Price
University of Warwick, UK.



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