verbose debugging requested, listing all options and arguments. option: addhLog , argument: addh.log option: addhydrogensDict , argument: reduce_wwPDB_het_dict.txt option: addhydrogensFirst , argument: True option: addhydrogensFirstOptions , argument: -OH -HIS -ALLALT -ROTNH3 -Keep option: addhydrogensOptions , argument: -OH -HIS -ALLALT -NOROTNH3 -Keep -METALBump1.5 -NONMETALBump-5.0 option: addhydrogensProgram , argument: private/reduce option: bindsiteResidues , argument: rec.site option: boxLog , argument: makebox.log option: boxOutput , argument: box option: boxProgram , argument: scripts/makebox.smallokay.pl option: boxRec , argument: False option: chargeFile , argument: amb.crg.oxt option: chargedPdbOutput , argument: rec.crg.pdb option: defaultFiles , argument: /raid1/people/rgc/Source/rgc_src/blast_defaultfiles option: doLigandDesolvation , argument: False option: doReceptorDesolvation , argument: False option: dockbase , argument: /raid1/people/rgc/Source/Dock/dockenv/trunk option: elecapp , argument: False option: filterLog , argument: filter.log option: filterParams , argument: filt.params option: filterProgram , argument: bin/Linux/filt.exe option: flexibleReadme , argument: flexible.explanation.txt option: flexibleResidues , argument: None option: indockName , argument: INDOCK option: ligand , argument: xtal-lig.pdb option: ligandDesolv , argument: ligand.desolv option: ligdesDir , argument: ligdes option: ligdesProbeRadius , argument: 1.8 option: ligdesTrimOut , argument: qnifft.ligdes.phi option: lowdielectricPdbLog , argument: lowdielectric.sph.pdb.log option: lowdielectricPdbOutput , argument: lowdielectric.sph.pdb option: lowdielectricSpheresLog , argument: lowdielectric.spheres.log option: lowdielectricSpheresOutput , argument: lowdielectric.sph option: lowdielectricSpheresProgram , argument: scripts/makespheres1.cli.pl option: matchingSpheresDist1 , argument: 1.5 option: matchingSpheresDist2 , argument: 0.8 option: matchingSpheresLog , argument: matching_spheres.log option: matchingSpheresMax , argument: 45 option: matchingSpheresOutput , argument: matching_spheres.sph option: matchingSpheresProgram , argument: scripts/makespheres3.cli.pl option: minLowdielectricSpheres , argument: 25 option: msLog , argument: dms.log option: msOutput , argument: rec.ms option: msProgram , argument: private/dms option: nearbyDir , argument: nearby option: nearbyOutside , argument: 3 option: nearbySkip , argument: 3 option: outputDir , argument: dockfiles option: partReadme , argument: part.explanation.txt option: pdbsphOutput , argument: xtal-lig.match.sph option: pdbsphProgram , argument: bin/Linux/pdbtosph option: qnifftGrid , argument: 193 option: qnifftLog , argument: qnifft.log option: qnifftOut , argument: qnifft.electrostatics.phi option: qnifftPdbOut , argument: qnifft.atm option: qnifftProgram , argument: bin/Linux/qnifft22_193_pgf_32 option: qnifftTrimOut , argument: trim.electrostatics.phi option: radiusFile , argument: vdw.siz option: recdesDir , argument: recdes option: recdesPdbOut , argument: qnifft.recdes.atm option: recdesProbeRadius , argument: 1.8 option: recdesTrimOut , argument: qnifft.recdes.phi option: receptor , argument: rec.pdb option: receptorLowdielectricOutput , argument: receptor.crg.lowdielectric.pdb option: solvmapHeavyName , argument: .heavy option: solvmapHeavyRadius , argument: 1.8 option: solvmapHydrogenName , argument: .hydrogen option: solvmapHydrogenRadius , argument: 1.0 option: solvmapLog , argument: solvmap.log option: solvmapProbeRadius , argument: 1.4 option: solvmapProgram , argument: bin/Linux/newsolv.sev option: sphgenOutput , argument: all_spheres.sph option: sphgenProgram , argument: bin/Linux/sphgen option: sphtopdbProgram , argument: etc/doshowsph.csh option: useFlex , argument: False option: useSge , argument: True option: vdwLog , argument: vdw.log option: vdwParameters , argument: vdw.parms.amb.mindock option: vdwPrefix , argument: vdw option: vdwProgram , argument: bin/Linux/chemgrid option: vdwProteinTable , argument: prot.table.ambcrg.ambH option: verbose , argument: True option: workingDir , argument: working copying input files into working directory, fixing columns rec.pdb xtal-lig.pdb working getting the most occupied position of each residue, renaming renaming HETATM to ATOM in the xtal-lig.pdb file running add hydrogens program command: cd working ; (/raid1/people/rgc/Source/Dock/dockenv/trunk/private/reduce -db reduce_wwPDB_het_dict.txt -OH -HIS -ALLALT -NOROTNH3 -Keep -METALBump1.5 -NONMETALBump-5.0 rec.pdb > rec.crg.pdb.fullh ) >& addh.log removing extraneous output from rec.crg.pdb.fullh command:cd working ; sed -i 's/\s*new\s*//g' rec.crg.pdb.fullh ; sed -i '/^USER.*/d' rec.crg.pdb.fullh adding hydrogens ran OK removing nonpolar hydrogens, renaming histidines, writing to working/rec.crg.pdb running filter program to create list of binding site residues command: cd working ; /raid1/people/rgc/Source/Dock/dockenv/trunk/bin/Linux/filt.exe < /raid1/people/rgc/Source/rgc_src/blast_defaultfiles/filt.params > filter.log filter program produced a list of binding site residue OK copying radii file /raid1/people/rgc/Source/rgc_src/blast_defaultfiles/radii to: working running molecular surface program command: cd working ; /raid1/people/rgc/Source/Dock/dockenv/trunk/private/dms rec.crg.pdb -a -i rec.site -g dms.log -p -n -o rec.ms molecular surface program ran OK running sphere generation program command: cd working ; /raid1/people/rgc/Source/Dock/dockenv/trunk/bin/Linux/sphgen sphere generation program ran OK running pdb to sphere program on ligand atoms command: cd working ; /raid1/people/rgc/Source/Dock/dockenv/trunk/bin/Linux/pdbtosph xtal-lig.pdb xtal-lig.match.sph ligand atom to sphere program ran OK running low dielectric spheres program command: cd working ; /raid1/people/rgc/Source/Dock/dockenv/trunk/scripts/makespheres1.cli.pl xtal-lig.match.sph all_spheres.sph rec.crg.pdb lowdielectric.sph 25 >& lowdielectric.spheres.log low dielectric spheres ran OK running sphere to pdb program command: cd working ; /raid1/people/rgc/Source/Dock/dockenv/trunk/etc/doshowsph.csh lowdielectric.sph 1 lowdielectric.sph.pdb >& lowdielectric.sph.pdb.log sphere to pdb ran OK running matching spheres program command: cd working ; /raid1/people/rgc/Source/Dock/dockenv/trunk/scripts/makespheres3.cli.pl 1.5 0.8 45 xtal-lig.match.sph all_spheres.sph rec.crg.pdb matching_spheres.sph >& matching_spheres.log matching spheres ran OK running makebox program command: cd working ; /raid1/people/rgc/Source/Dock/dockenv/trunk/scripts/makebox.smallokay.pl matching_spheres.sph rec.crg.pdb box >& makebox.log make box ran OK running concatenate program command: cd working ; cat rec.crg.pdb lowdielectric.sph.pdb > receptor.crg.lowdielectric.pdb concatenate program ran OK running qnifft program command: cd working ; /raid1/people/rgc/Source/Dock/dockenv/trunk/bin/Linux/qnifft22_193_pgf_32 qnifft.parm >& qnifft.log qnifft.parm parameter file follows: grid=193 charge=amb.crg.oxt radius=vdw.siz pdb_input=receptor.crg.lowdielectric.pdb pdb_output_file=qnifft.atm phi_output_file=qnifft.electrostatics.phi qnifft.parm parameter file ends. qnifft program ran OK running vdw program command: cd working ; /raid1/people/rgc/Source/Dock/dockenv/trunk/bin/Linux/chemgrid >& vdw.log INCHEM parameter file follows: rec.crg.pdb prot.table.ambcrg.ambH vdw.parms.amb.mindock box 0.33 1 4 10 2.3 2.6 vdw INCHEM parameter file ends. vdw program ran OK making temporary solvmap directory working/heavy copying files into working/heavy : rec.crg.pdb box running ligand desolvation program command: cd working/heavy ; /raid1/people/rgc/Source/Dock/dockenv/trunk/bin/Linux/newsolv.sev >& solvmap.log INSEV parameter file follows: rec.crg.pdb ligand.desolv.heavy 1.60,1.65,1.90,1.90,1.90,1.60 1.4 2 box 1.8 INSEV parameter file ends. ligand desolvation program ran OK making temporary solvmap directory working/hydrogen copying files into working/hydrogen : rec.crg.pdb box running ligand desolvation program command: cd working/hydrogen ; /raid1/people/rgc/Source/Dock/dockenv/trunk/bin/Linux/newsolv.sev >& solvmap.log INSEV parameter file follows: rec.crg.pdb ligand.desolv.hydrogen 1.60,1.65,1.90,1.90,1.90,1.60 1.4 2 box 1.0 INSEV parameter file ends. ligand desolvation program ran OK copying matching_spheres.sph into dockfiles copying trim.electrostatics.phi into dockfiles copying ligand.desolv.hydrogen into dockfiles copying ligand.desolv.heavy into dockfiles copying vdw.bmp into dockfiles copying vdw.vdw into dockfiles copying vdw.parms.amb.mindock into dockfiles writing INDOCK file: INDOCK