minimization/scoring script

[dkoes]

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).

[magsol]

What lines did you comment out?

[Proto]

#($r2h, $r2name) = tempfile(SUFFIX=>'.pdbqt');
#system("babel $rec $rname");
#convert to pdbqt
#system("$SCRIPTPATH/prepare_receptor4.py -r $rname -o $r2name 2>&1");

You also have to change all instances of r2name for rec