Proto wrote:I see. Sorry for the slipup. However that in turn revealed the real problem I was having before I started printing the output...
Cannot read input format ".pdbqt" for file "3ECH_AB.pdbqt"
It'd appear babel cannot handle pdbqt? A quick look at babel -H doesn't seem to list it.
Hmm.. I'm running babel 2.3.0. You can either upgrade or, since you're starting with a pdbqt file to begin with anyway, you could change babel to cp and it should just work (in fact you could remove the whole prepare_receptor bit, but that requires a little more thought).