ADL: can't find or open *.receptor.C.map

Bernhard Knapp bernhard.knapp at meduniwien.ac.at
Fri Jan 18 05:38:44 PST 2008


Dear autodockers

I am novice in using autodock. My aim is to score my receptor/ligand 
complexes where the binding side is almost known (so pure scoring just 
with a little induced fit would be perfect). Most autodock tutorials are 
using ADT which seems not to be the appropriate way for me becauce 
manual user input is needed. So I came over the "VI European Workshop on 
Drug Design - Molecular Docking Tutorial" which also offers shortcuts 
via python scripts. I tried to get this one running for one of my 
complexes and it works fine except the last (and most important) 
autodock call:

/home/bknapp/MGLTools-1.4.6/share/bin/pythonsh 
/home/bknapp/MGLTools-1.4.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py 
-l complexLLFGAPVYV.ligand.pdb -o complexLLFGAPVYV.ligand.pdbqt
/home/bknapp/MGLTools-1.4.6/share/bin/pythonsh 
/home/bknapp/MGLTools-1.4.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py 
-r complexLLFGAPVYV.receptor.pdb -o complexLLFGAPVYV.receptor.pdbqt

/home/bknapp/downloads/autoDock_4/autodocktools/pdbbox 
complexLLFGAPVYV.ligand.pdb | egrep "REMARK|HETATM|CONECT|END" > box.pdb

/home/bknapp/MGLTools-1.4.6/share/bin/pythonsh 
/home/bknapp/MGLTools-1.4.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_gpf4.py 
-o complexLLFGAPVYV.gpf -l complexLLFGAPVYV.ligand.pdbqt -r 
complexLLFGAPVYV.receptor.pdbqt -p ligand_types="A C Cl H F OA N P S Br 
NA SA HD" -p gridcenter="grid center coordinates" -p npts="grid points"

/home/bknapp/downloads/autoDock_4/i86Linux2/autogrid4 -p 
complexLLFGAPVYV.gpf -l complexLLFGAPVYV.glg

/home/bknapp/MGLTools-1.4.6/share/bin/pythonsh 
/home/bknapp/MGLTools-1.4.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_dpf4.py 
-l complexLLFGAPVYV.ligand.pdbqt -r complexLLFGAPVYV.receptor.pdbqt -p 
ga_run=100 -o complexLLFGAPVYV.dpf

/home/bknapp/downloads/autoDock_4/i86Linux2/autodock4 -p 
complexLLFGAPVYV.dpf -l complexLLFGAPVYV.dlg


if executing the last line it says:
"I'm sorry; I can't find or open  "complexLLFGAPVYV.receptor.C.map"

which is obviously clear because this file is not existing, only 
complexLLFGAPVYV.receptor.A.map, complexLLFGAPVYV.receptor.d.map, 
complexLLFGAPVYV.receptor.e.map are there.



Can anyone help with that?


Regards,
Bernhard







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