Conversion from XML to DLG

[MicheleRoggia]

Hi everyone,
I have a problem when trying to convert XML to DLG files using AutoDockGPU.

When launching the command "AD4_GPU_A6K --xml2dlg ligand_name.xml" the following error is reported:

AutoDock-GPU version: v1.5-release

Converting 1 xml file to dlg

Error: No ligand or flex res file specified.

Error in init_liganddata, stopped job.

Error in setup of Job #1:
( Grid map file: )
( Ligand file: )
Run time of entire job set (1 file): 0.001 sec
Processing time: 0.000 sec

Warning: The following jobs were not successful:
Job 0: ligand_name.pdbqt

I already checked for the path of both "Grid map file" and "Ligand file" and everything seems to be ok.

Is there any way to solve this issue?

Thanks
MR

[atillack]

@MicheleRoggia I am trying to come up with a way to reproduce the error but so far am unsuccessful (based on the error message this has to be v1.6 - GitHub sometimes sticks to the old version). Could you please post the first couple of lines in the xml file until the <runs> keyword - and of course, please redact your filenames but indicate something is there (i.e. xyz.pdbqt, M.maps.fld - also, the <arguments> keyword contains the entire command line).

My suspicion currently is this might have been a covalent run?

[MicheleRoggia]

Dear @atillack, thank you for your quick reply. Here you can find the requested xml content.

<autodock_gpu>
v1.5-release
-ffile /home/user/user_data/Receptor_name/Receptor/PDB_prepared.maps.fld -lfile /data01/Dataset/ligand_name.pdbqt -nrun 50 -heuristics 1 -devnum 2 -resnam ligand_name -d 0
/home/user/user_data/Receptor_name/Receptor/PDB_prepared.maps.fld
/data01/Dataset/ligand_name.pdbqt
1738837484 65602
<ls_method>ad</ls_method>
yes
yes
<run_requested>50</run_requested>

Anyway I solved this first issue by using /bin/autodock_gpu_128wi instead of the already compiled "AD4_GPU_A6K". Now, when I try to visualize the DLG file by using ADT GUI, it returns me this error:

Traceback (most recent call last):
File "/opt/MGLTools-1.5.7/MGLToolsPckgs/ViewerFramework/VF.py", line 941, in tryto
result = command( *args, **kw )
File "/opt/MGLTools-1.5.7/MGLToolsPckgs/AutoDockTools/autoanalyzeCommands.py", line 3860, in doit
d.readDlg(dlgFile)
File "/opt/MGLTools-1.5.7/MGLToolsPckgs/AutoDockTools/Docking.py", line 96, in readDlg
dlo = DockingLogObject(self, dlgFile)
File "/opt/MGLTools-1.5.7/MGLToolsPckgs/AutoDockTools/Docking.py", line 728, in init
parser.parse(filename)
File "/opt/MGLTools-1.5.7/MGLToolsPckgs/AutoDockTools/DlgParser.py", line 121, in parse
self.match(allLines)
File "/opt/MGLTools-1.5.7/MGLToolsPckgs/AutoDockTools/DlgParser.py", line 236, in match
apply(d['func'], (lines,), {})
File "/opt/MGLTools-1.5.7/MGLToolsPckgs/AutoDockTools/DlgParser.py", line 762, in getModelLines
for i in range(self.runs):
AttributeError: DlgParser instance has no attribute 'runs'

I also tried to relauch the docking on a single ligand using /bin/autodock_gpu_128wi but still I had the same error

[atillack]

@MicheleRoggia Thank you for reporting back - I am glad recompiling fixed the issue. I'll forward the issue to the MGLTools developer - it looks like it didn't read the ga_run dpf entry that is placed in the dlg.

[MicheleRoggia]

@atillack Thank you so much. I'll wait for developer support