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I'm trying to do a specific docking for a protein that already has a co-crystalized ligand attached to it. However, I'm not sure what method to use.

After searching online, I found out that I should identify the interacting residues of that ligand. Then, I have opened this protein-ligand complex in 2 applications and 1 web server.

Here are the information of the protein-ligand complex:

• The protein PDB ID is: 5TL8 (Naegleria fowleri CYP51-posaconazole complex)
• The ligand is Posaconazole
• The cofactor and other small molecules: HEME, 1,2-ETHANEDIOL, calcium ion

I tried opening the complex in Discovery Studio Ligplus

and Protein Plus webserver (this server has more interacting residues). All of them have different residues.

Which one should I follow? Should we included the HEME or do we just look at the Posaconazole itself?

I'm trying to do a specific molecular docking using Autodock Vina in PyRx. So, one way to do that is to mark all of the interacting residues and make sure the grid box encompasses all of that interacting residues.

So, my protein already has a co-crystalized ligand attached to it. However, I'm not sure what method to use.

After searching online, I found out that I should identify the interacting residues of that ligand. Then, I have opened this protein-ligand complex in 2 applications and 1 web server.

Here are the information of the protein-ligand complex:

• The protein PDB ID is: 5TL8 (Naegleria fowleri CYP51-posaconazole complex)
• The ligand is Posaconazole
• The cofactor and other small molecules: HEME, 1,2-ETHANEDIOL, calcium ion

I tried opening the complex in Discovery Studio Ligplus

and Protein Plus webserver (this server has more interacting residues). All of them have different residues.

Which one should I follow? Should we included the HEME or do we just look at the Posaconazole itself?

I'm trying to do a specific docking for a protein that already has a co-crystalized ligand attached to it. However, I'm not sure what method to use.

After searching online, I found out that I should identify the interacting residues of that ligand. Then, I have opened this protein-ligand complex in 2 applications and 1 web server.

Here are the information of the protein-ligand complex:

• The protein PDB ID is: 5TL8 (Naegleria fowleri CYP51-posaconazole complex)
• The ligand is Posaconazole
• The cofactor and other small molecules: HEME, 1,2-ETHANEDIOL, calcium ion

I tried opening the complex in Discovery Studio Ligplus

and Protein Plus webserver (this server has more interacting residues). All of them have different residues. Which one should I follow?

I'm trying to do a specific docking for a protein that already has a co-crystalized ligand attached to it. However, I'm not sure what method to use.

After searching online, I found out that I should identify the interacting residues of that ligand. Then, I have opened this protein-ligand complex in 2 applications and 1 web server.

Here are the information of the protein-ligand complex:

• The protein PDB ID is: 5TL8 (Naegleria fowleri CYP51-posaconazole complex)
• The ligand is Posaconazole
• The cofactor and other small molecules: HEME, 1,2-ETHANEDIOL, calcium ion

I tried opening the complex in Discovery Studio Ligplus

and Protein Plus webserver (this server has more interacting residues). All of them have different residues. 

Which one should I follow? Should we included the HEME or do we just look at the Posaconazole itself?