#3 Error save function for "Save Docked Complex as PDB"

[Broto Santoso]

Dear Sarkis,

Long time no see. I have emailed you before this about the question: Have PyRx's forum been shutting down?
And I have a problem, when I want to use new feature in 0.9.4 "Save Docked Complex as PDB", I got this message

Traceback (most recent call last):
  File "/Library/PyRx/0.9.2/Python.framework/Versions/2.6/lib/python2.6/site-packages/PyRx/analyzePage.py", line 281, in OnSaveComplex
    writer.write("pyrx_tmpfile.pdb", mol, records=['ATOM', 'HETATM'])                
  File "/Library/PyRx/0.9.2/Python.framework/Versions/2.6/lib/python2.6/site-packages/MolKit/pdbWriter.py", line 92, in write
    assert isinstance(nodes, TreeNode) or isinstance(nodes, TreeNodeSet)
AssertionError

I need your assisstance. Thank you

regard

bsantoso

[Broto Santoso]

one more question, when I run AutoDock Wizard, I got this message:

DPF> map ../3hb5_nw_protein.A.map            # atom-specific affinity map~~~


/Library/PyRx/0.9.2/bin/autodock4: WARNING: Filename mismatch: "3hb5_nw_protein.maps.fld" :: "../3hb5_nw_protein.maps.fld"
DPF> map ../3hb5_nw_protein.C.map            # atom-specific affinity map

/Library/PyRx/0.9.2/bin/autodock4: WARNING: Filename mismatch: "3hb5_nw_protein.maps.fld" :: "../3hb5_nw_protein.maps.fld"
DPF> map ../3hb5_nw_protein.OA.map           # atom-specific affinity map

/Library/PyRx/0.9.2/bin/autodock4: WARNING: Filename mismatch: "3hb5_nw_protein.maps.fld" :: "../3hb5_nw_protein.maps.fld"
DPF> map ../3hb5_nw_protein.HD.map           # atom-specific affinity map

/Library/PyRx/0.9.2/bin/autodock4: WARNING: Filename mismatch: "3hb5_nw_protein.maps.fld" :: "../3hb5_nw_protein.maps.fld"
DPF> map ../3hb5_nw_protein.N.map            # atom-specific affinity map

/Library/PyRx/0.9.2/bin/autodock4: WARNING: Filename mismatch: "3hb5_nw_protein.maps.fld" :: "../3hb5_nw_protein.maps.fld"
DPF> elecmap ../3hb5_nw_protein.e.map        # electrostatics map

/Library/PyRx/0.9.2/bin/autodock4: WARNING: Filename mismatch: "3hb5_nw_protein.maps.fld" :: "../3hb5_nw_protein.maps.fld"
DPF> desolvmap ../3hb5_nw_protein.d.map      # desolvation map

/Library/PyRx/0.9.2/bin/autodock4: WARNING: Filename mismatch: "3hb5_nw_protein.maps.fld" :: "../3hb5_nw_protein.maps.fld"
DPF> move ../../../Ligands/3hb5_nw_ligand.pdbqt  # small molecule

In Mac the process still continue. But the same thing happened in Windows, make the autodock4 stopped.
The Questions: Is it normal when you used AutoDock? and how to solve the windows' problem?

Thanks

regard
bsantoso

[Sarkis Dallakian]

You can safely ingnore this WARNING messages. It might be that the Windows computer has less memory than the Mac. Can you send me the input files and the specs of Mac and Windows computers so I can look into this further.

Thanks,
Sarkis

[Sarkis Dallakian]

Dear Broto,

Thanks for the message. I see that http://mgl.scripps.edu/forum/ errors out and I don't know if or when it will be fixed. I have been meaning to move the discussions to SourceForge and this might be a good time to do it.

For the error with "Save Docked Complex as PDB" can you please zip the receptor folder and send me the files so I can look into it.

I'll be happy to fix this if I can reproduce this on my end.

Thank you!