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Error in PyRx while using open babel to convert small molecules to...
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+ Bioinformatic software
+ Autodock
+ Virtual screening
+ Molecular docking
+ Autodock vina
+ Bioinformatics
+ Small molecules
Posted by
Laura Miller
Error in PyRx while using open babel to convert small molecules to...
Best way to get .pdbqt of a small molecule is following. 1. Draw the structure of your molecule in ChemDraw and put the structure in the chem3D (a sister software of ChemDraw freely available with it). 2. Go to calculation --> MM--> energy minimize --> run. Save the optimized structure of the molecule in .mol2 3. Open AutoDock tools --> ligand --> open your mol2 file. Then ligand --> chose torsions. Again go ligand and save it as .pdbqt file.
It is the best because the .pdbqt file will not give any error in further calculations.
Best way to get .pdbqt of a small molecule is following. 1. Draw the structure of your molecule in ChemDraw and put the structure in the chem3D (a sister software of ChemDraw freely available with it). 2. Go to calculation --> MM--> energy minimize --> run. Save the optimized structure of the molecule in .mol2 3. Open AutoDock tools --> ligand --> open your mol2 file. Then ligand --> chose torsions. Again go ligand and save it as .pdbqt file.
It is the best because the .pdbqt file will not give any error in further calculations.
Partial charge addition Energy minimization Correct geometry if required If you have drawn the structure kindly check in chemdraw if its ok (if downloaded from then not required)
Partial charge addition Energy minimization Correct geometry if required If you have drawn the structure kindly check in chemdraw if its ok (if downloaded from then not required)
Convert your .sdf file directly using openbabel to mol2 and then .pdbqt. Hope it would work, sometime openbabel gives this error when you are asking for the same (not supported format). Secondly, if this also don't work kindly convert your .sdf to .pdb and convert it to .pdbqt using autodock. Good luck Julia Gomes
Convert your .sdf file directly using openbabel to mol2 and then .pdbqt. Hope it would work, sometime openbabel gives this error when you are asking for the same (not supported format). Secondly, if this also don't work kindly convert your .sdf to .pdb and convert it to .pdbqt using autodock. Good luck Julia Gomes
While converting to pdbqt you must add charge and atom type. It is always better to convert sdf to pdb first. Then add charges and assign atom types using any software like autodock and then write the pdbqt file.
While converting to pdbqt you must add charge and atom type. It is always better to convert sdf to pdb first. Then add charges and assign atom types using any software like autodock and then write the pdbqt file.
Best way to get .pdbqt of a small molecule is following.
1. Draw the structure of your molecule in ChemDraw and put the structure in the chem3D (a sister software of ChemDraw freely available with it).
2. Go to calculation --> MM--> energy minimize --> run. Save the optimized structure of the molecule in .mol2
3. Open AutoDock tools --> ligand --> open your mol2 file. Then ligand --> chose torsions. Again go ligand and save it as .pdbqt file.
It is the best because the .pdbqt file will not give any error in further calculations.
Best way to get .pdbqt of a small molecule is following.
1. Draw the structure of your molecule in ChemDraw and put the structure in the chem3D (a sister software of ChemDraw freely available with it).
2. Go to calculation --> MM--> energy minimize --> run. Save the optimized structure of the molecule in .mol2
3. Open AutoDock tools --> ligand --> open your mol2 file. Then ligand --> chose torsions. Again go ligand and save it as .pdbqt file.
It is the best because the .pdbqt file will not give any error in further calculations.
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You can try the following۔۔۔
Partial charge addition
Energy minimization
Correct geometry if required
If you have drawn the structure kindly check in chemdraw if its ok (if downloaded from then not required)
Then try
You can try the following۔۔۔
Partial charge addition
Energy minimization
Correct geometry if required
If you have drawn the structure kindly check in chemdraw if its ok (if downloaded from then not required)
Then try
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Convert your .sdf file directly using openbabel to mol2 and then .pdbqt. Hope it would work, sometime openbabel gives this error when you are asking for the same (not supported format).
Secondly, if this also don't work kindly convert your .sdf to .pdb and convert it to .pdbqt using autodock.
Good luck Julia Gomes
Convert your .sdf file directly using openbabel to mol2 and then .pdbqt. Hope it would work, sometime openbabel gives this error when you are asking for the same (not supported format).
Secondly, if this also don't work kindly convert your .sdf to .pdb and convert it to .pdbqt using autodock.
Good luck Julia Gomes
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While converting to pdbqt you must add charge and atom type. It is always better to convert sdf to pdb first. Then add charges and assign atom types using any software like autodock and then write the pdbqt file.
While converting to pdbqt you must add charge and atom type. It is always better to convert sdf to pdb first. Then add charges and assign atom types using any software like autodock and then write the pdbqt file.
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Open babel to convert first pdbq and then proceeds in auto dock tool to prepare protein as pdbqt by follow step as explain nayim
Open babel to convert first pdbq and then proceeds in auto dock tool to prepare protein as pdbqt by follow step as explain nayim
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