ADL: ATOM and HETATM Records

Jack Shultz jshultz at hydrogenathome.org
Mon Jun 1 17:58:31 PDT 2009


I had the same result with the recent download of MGLTools and Autodock4

C:\Users\jshultz\test>prepare_ligand4.py -l ligand.mol2 -o ligand.pdbqt

C:\Users\jshultz\test>prepare_receptor4.py -U nphs_lps_waters -r receptor.pdb -o
 receptor.pdbqt
adding gasteiger charges to peptide

C:\Users\jshultz\test>prepare_flexdocking4.py -l ligand.pdbqt -r receptor.pdbqt
-g receptor_rigid.pdbqt -x receptor_flex.pdbqt -s receptor:A:TYR48_PHE86_ILE95_L
EU97_TYR100_LEU104_GLN141_MET149_receptor:B:LYS102_GLN141_ASN143_ASP145_THR146_L
EU147

C:\Users\jshultz\test>prepare_gpf4.py  -l ligand.pdbqt -r receptor_rigid.pdbqt -
p custom_parameter_file=1 -p parameter_file=AD4_parameters.dat -p ligand_types="
A C HD N NA OA SA"
setting ligand_types: newvalue= A C HD N NA OA SA

C:\Users\jshultz\test>prepare_dpf4.py -l ligand.pdbqt -r receptor_rigid.pdbqt -p
 compute_unbound_extended_flag=0 -p ga_run=10 -p flexres=receptor_flex.pdbqt

C:\Users\jshultz\test>autogrid4.exe  -p receptor_rigid.gpf -l out.glg

autogrid4: Successful Completion.

C:\Users\jshultz\test>autodock4.exe  -p ligand_receptor_rigid.dpf -l out.dlg
autodock4: ERROR:  All ATOM and HETATM records must be given before any nested B
RANCHes; see line 194 in PDBQT file "ligand.pdbqt".
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