Question

Asked 27 December 2023

Tarbiat Modares University

Zerodivisionerror error in autodock?

Hi, I used material studio and biuld selnium nanoparticle. I used autodock and dock nanoparticle with hsa . when input ligand I recieved this error.

Python 2.5.2 (r252:60911, Feb 21 2008, 13:11:45) [MSC v.1310 32 bit (Intel)] on win32

Type "copyright", "credits" or "license()" for more information.

****************************************************************

Personal firewall software may warn about the connection IDLE

makes to its subprocess using this computer's internal loopback

interface. This connection is not visible on any external

interface and no data is sent to or received from the Internet.

****************************************************************

IDLE 1.2.2 ==== No Subprocess ====

>>> adding gasteiger charges to receptor

NanoSe3: :MOL2:Se and NanoSe3: :MOL2:Se have the same coordinates

ERROR *********************************************

Traceback (most recent call last):

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto

result = command( *args, **kw )

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autotorsCommands.py", line 1008, in doit

initLPO4(mol, cleanup=cleanup)

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autotorsCommands.py", line 292, in initLPO4

root=root, outputfilename=outputfilename, cleanup=cleanup)

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 1019, in __init__

detect_bonds_between_cycles=detect_bonds_between_cycles)

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 768, in __init__

delete_single_nonstd_residues=False)

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 143, in __init__

self.addCharges(mol, charges_to_add)

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 229, in addCharges

chargeCalculator.addCharges(mol.allAtoms)

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\MolKit\chargeCalculator.py", line 80, in addCharges

babel.assignHybridization(atoms)

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\PyBabel\atomTypes.py", line 137, in assignHybridization

self.valence_two()

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\PyBabel\atomTypes.py", line 266, in valence_two

angle1 = bond_angle(k.coords, a.coords, l.coords)

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\PyBabel\util.py", line 47, in bond_angle

raise ZeroDivisionError("Input used:", a, b, c)

ZeroDivisionError: ('Input used:', [-3.7719999999999998, -9.9429999999999996, -5.774], [-3.7719999999999998, -9.9429999999999996, -5.774], [-3.7719999999999998, -9.9429999999999996, -5.774])

Salvatore Galati

University of Pisa

Hello,

It appears that there are two selenium atoms that have the same coordinates. This is a problem for the preparation script as it is not possible to determine the hybridization of these two atoms. I recommend that you check the structure of your input files to make sure there are no errors.

Cite

Elahe Siadati

Tarbiat Modares University

Hi tanks a lot. I appreciate that.

Cite

MGLTools 1.5.7 (AutodockTools) on Windows 10 throwing a python stack trace. Why?

Question

7 answers

Asked 9 June 2021

Anthony Nash

First, I've had MGLTools on Windows 10 working fine up until today. Unfortunately, it was about 4 months ago since I last opened it and I forgot the *hack* that was required.

Here is the problem. I've installed AutodockTools (MGLTools - or which order it comes in) and despite it working once before I can't get it to open. This is the error:

Python 2.7.11 (v2.7.11:6d1b6a68f775, Dec 5 2015, 20:32:19) [MSC v.1500 32 bit (Intel)] on win32

Type "copyright", "credits" or "license()" for more information.

==== No Subprocess ====

>>> Traceback (most recent call last):

File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\__init__.py", line 433, in runADT

title=title, withShell= not interactive, verbose=False, gui=gui)

File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\Pmv\moleculeViewer.py", line 1026, in __init__

trapExceptions=trapExceptions)

File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\ViewerFramework\VF.py", line 523, in __init__

self.userpref.loadSettings()

File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\mglutil\preferences.py", line 138, in loadSettings

self.set(key, value)

File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\mglutil\preferences.py", line 107, in set

cb(name,oldValue, value)

File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\ViewerFramework\VF.py", line 760, in startupDirPref_cb

root = self.setUserPreference.form.root

AttributeError: SetUserPreference instance has no attribute 'form'

hit enter to continue

Any idea what on earth is going on? A few things to note.

This seems to be trying to launch Python 2.7. The software is also packaged with that version of Python itself (wow, that strikes me as very strange). I tried using Python 3.8, and predictably it did nothing.

Working solutions welcome.

"prot:A:MET1:HN1 and prot:A:MET1:HN1 have the same coordinates" Error While Performing Flexible Docking?

Question

1 answer

Asked 29 December 2022

Anusha Majumder

After selecting the residues of the protein for flexible docking, when I click on "Choose Torsions In Currently Selected Residues", under the " Flexible Residues" tab, I get this error:

prot:A:MET1:HN1 and prot:A:MET1:HN1 have the same coordinates

ERROR *********************************************

Traceback (most recent call last):

File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\ViewerFramework\VF.py", line 941, in tryto

result = command( *args, **kw )

File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\autoflexCommands.py", line 369, in doit

map(self.setAutoFlexFields, flex_residues)

File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\autoflexCommands.py", line 414, in setAutoFlexFields

rotatables = rbs.select(bondlist)

File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\MolKit\bondSelector.py", line 534, in select

rotatable = BondOrderBondSelector().select(bnds,1)

File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\MolKit\bondSelector.py", line 507, in select

atype.assignHybridization(allAts)

File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\PyBabel\atomTypes.py", line 137, in assignHybridization

self.valence_two()

File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\PyBabel\atomTypes.py", line 266, in valence_two

angle1 = bond_angle(k.coords, a.coords, l.coords)

File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\PyBabel\util.py", line 47, in bond_angle

raise ZeroDivisionError("Input used:", a, b, c)

ZeroDivisionError: ('Input used:', [2.015, -1.769, 0.66], [2.015, -1.769, 0.66], [2.015, -1.769, 0.66])

Is there a way to solve this problem?

Can any one help me in resolving this error generated during macromolecule preparation?

Question

8 answers

Asked 28 June 2021

Kirti Wasnik

ERROR Cannot create the PDBQT file, all atoms do not have an autodock_element field

.pdbqt file is not generating.

Autogrid4 show IDLE 1.2.2 No Subprocess ?

Question

6 answers

Asked 26 December 2016

Xyztlik Shawn

Hi, i am trying to do autogrid using autodock tool. But having this error as below:

Can someone pls explain how can i avoid this error. e look to other posts but still cant solve this error. Pls advice. Thanks in advance.

Python 2.5.2 (r252:60911, Feb 21 2008, 13:11:45) [MSC v.1310 32 bit (Intel)] on win32

Type "copyright", "credits" or "license()" for more information.

****************************************************************

Personal firewall software may warn about the connection IDLE

makes to its subprocess using this computer's internal loopback

interface. This connection is not visible on any external

interface and no data is sent to or received from the Internet.

****************************************************************

IDLE 1.2.2 ==== No Subprocess ====

>>> Exception in Tkinter callback

Traceback (most recent call last):

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\lib-tk\Tkinter.py", line 1403, in __call__

return self.func(*args)

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\Pmv\guiTools.py", line 350, in do_1

self.kill(e.widget.get(e.widget.nearest(e.y)))

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autostartCommands.py", line 144, in kill

if self.manager.processCts[prog]>0:

KeyError: 'Program'

How to prepare ligand file for autodock which gives error ligand: :UNK0:Nd and ligand: :UNK0:Nd have the same coordinates?

Question

11 answers

Asked 8 August 2023

Piyush Kumar

I have been trying to dock a certain protein with nd ion i downloaded from rcsb but after i add it to pyrx and try to convert it to ligand i get the following error. I tried converting the sdf file to pdb using pymol, chimeraX, avogadro, open babel but even then when i open the file it gives me this error: ligand: :UNK0:Nd and ligand: :UNK0:Nd have the same coordinates. Could someone please help?

Update: I want to dock an unbound protein with the neodymium metal ion which i downloaded from rcsb in sdf format and later tried to convert it to pdb using the aforementioned softwares for autodock to accept it but i can't get it to be accepted by autodock as a proper ligand. Apparently I am unable to get any of the rare earth elements to be accepted properly as ligands.

What is a good docking score?

Question

7 answers

Asked 12 April 2022

Sumiran Ami Kapur

As I am new to docking part, wanted to know that is a more negative docking score in RMSD table is better or positive score is better.

As i have read two recent papers in which both are explaining different information related to docking.

I want the clarity in the docking score which better for research purpose?

Which molecules shows higher binding interactions in molecular docking?

Discussion

4 replies

Asked 14 March 2022

Bala Subramaniyan

Dear Researchers and Professors, recently I faced some doubt in molecular docking energy result. Herewith I have enclosed CDOCKER (Discovery studio software) energy values of some docked molecule. Generally in literature mentioned, negative docking energy values indicates more binding energy. In following attached image which molecule has more higher binding interactions? Kindly explain. My doubt is in the result table commonly mentioned (-CDOCKER energy). Means the all the positive values are considered as a negative value or not?. Some time the values shows in negative values.

How can I solve the following issue on Autodock vina "Parse error on line 2 in file "ligand.pdbqt": Unknown or inappropriate tag"?

Question

12 answers

Asked 6 April 2020

Mina Poursharifi

I have all the files ligand + receptor (both in pdbqt)+ all vina files vina.exe ,vina_license+vina split +conf txt in a single folder.

I keep getting this error when I try to run docking in command prompt. here I attached the picture of the error and my txt.

I am very new to this field, appreciate your help.

AutoDock Running Error?

Question

10 answers

Asked 25 February 2020

Susantha K Ganegamage

I have tried to run Autodock by following youtube video ( https://www.youtube.com/watch?v=llaVCIfH0sA ) but when I run AutoDock the error message comes. I have pasted the error message below please help me to fix this.

............................................................................................................................................

Python 2.5.2 (r252:60911, Feb 21 2008, 13:11:45) [MSC v.1310 32 bit (Intel)] on win32

Type "copyright", "credits" or "license()" for more information.

****************************************************************

Personal firewall software may warn about the connection IDLE

makes to its subprocess using this computer's internal loopback

interface. This connection is not visible on any external

interface and no data is sent to or received from the Internet.

****************************************************************

IDLE 1.2.2 ==== No Subprocess ====

>>> adding gasteiger charges to 3ec5

3ec5 already has gasteiger charges

ERROR *********************************************

Traceback (most recent call last):

File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto

result = command( *args, **kw )

File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autostartCommands.py", line 964, in doit

ps = subprocess.Popen(args)

File "C:\Program Files\MGLTools-1.5.6\lib\subprocess.py", line 594, in __init__

errread, errwrite)

File "C:\Program Files\MGLTools-1.5.6\lib\subprocess.py", line 816, in _execute_child

startupinfo)

WindowsError: [Error 740] The requested operation requires elevation

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Zerodivisionerror error in autodock?

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