Would you like to build a 3D structure for your target proteins..?

First, you open the .pdb file. Select the chain (A or B or C). Right click the "+' symbol and make the Macromolecule

Thank you selva... Tried that already but it's showing error to make macromolecule..

hi mr. Rajkumar, Did you get the answer?. in my work, it would be better if we docking it in 1 chain. you can do it with 2 chain, but mostly in some protein i got some error isues that same as you have.

Hello. I am facing an error when I click on "Make macromolecule". Any suggestions?

during the formation of "make macromolecule," I face the below error.

Traceback (most recent call last):

File "C:\Program Files (x86)\PyRx\lib\site-packages\PyRx\molNavigator.py", line 136, in OnMakeMacromolecule

mol = self.frame.autodockNav.AddMacromolecule(mol)

File "C:\Program Files (x86)\PyRx\lib\site-packages\PyRx\autodockNavigator.py", line 66, in AddMacromolecule

mol = self.SelectAlternate(mol)

File "C:\Program Files (x86)\PyRx\lib\site-packages\PyRx\autodockNavigator.py", line 143, in SelectAlternate

self.vsModel.PrepareReceptorMol(mol)

File "C:\Program Files (x86)\PyRx\lib\site-packages\PyRx\vsModel.py", line 358, in PrepareReceptorMol

RPO = AD4ReceptorPreparation(mol, outputfilename=outputfilename)

File "C:\Program Files (x86)\PyRx\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 546, in __init__

version=version, delete_single_nonstd_residues=delete_single_nonstd_residues)

File "C:\Program Files (x86)\PyRx\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 123, in __init__

self.repairMol(mol, self.repair_type_list)

File "C:\Program Files (x86)\PyRx\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 178, in repairMol

self.newHs = self.addHydrogens(mol)

File "C:\Program Files (x86)\PyRx\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 186, in addHydrogens

HB.addHydrogens(mol)

File "C:\Program Files (x86)\PyRx\lib\site-packages\MolKit\hydrogenBuilder.py", line 100, in addHydrogens

childIndex = res.children.index(heavyAtom)+1

File "C:\Program Files (x86)\PyRx\lib\UserList.py", line 81, in index

def index(self, item, *args): return self.data.index(item, *args)

ValueError: list.index(x): x not in list

If I am using a mutant protein and trying to convert it as macromolecule in pyrx I am getting the error, kindly let me know how to sort it.

First check the format, try changing format.

or else check how many chains are selected. since only one chain can be used for used and multiple chains are checked by default in pyrx so you uncheck that and use one chain and convert that protein into macromolecule.