Body: <p>I have been docking multiple ligands on a protein,the ligands were correct initially (without explicit hydrogen ATOMS all ligands were processed by same method) but some ligand poses show additional hydrogen atom in the ligand output whereas some ligands did not show explicit hydrogen atoms.</p>
  <p>I also tried using two docking platforms autodock vina as well as QVina.</p>
  <p>I have uploaded the ligand output one with no issue and other with explicit hydrogens.</p>
  <p><a href="https://i.sstatic.net/AjqCZd8J.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/AjqCZd8J.jpg" alt="Ligands pose output" /></a></p>
  <p>We received additional hydrogen along with ligands as you can see in second image and before docking the ligand is normal (image 1). So here is what we perform firstly we optimize the ligand structure using RDKit and apply the MMFF (Merck Molecular Force Field) for energy minimization. Subsequently, perform molecular docking using QVina to produce this output.</p>
  <p>Why did this happen and how do I solve this?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-12-11T10:04:20.977Z
Comments.Text: Why is this question tagged with chimera?
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-12-11T11:43:57.870Z
Comments.Text: plz provide solution
Comments.UserDisplayName: Dikshit Rathva
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-12-11T19:08:26.140Z
Comments.Text: I don't know enough about the problem to be able to provide a good solution. I'm trying to help you improve your question, so that someone who *does* know about this domain can give a better answer.
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-12-11T19:32:38.333Z
Comments.Text: please provide at least two ligannds and describe the procedure that gave out two different kind of results
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-12-11T19:33:20.310Z
Comments.Text: cant you just feed the algho with ligand already contining explicit Hs provided by third party procedure ??
Comments.UserDisplayName: pippo1980
Tags: <protein-structure><docking><chimera><autodock>
Title: Molecular Docking
ThreadText: # Molecular Docking
  
  (Asked by: username_0 on 2024-12-10)
  
  I have been docking multiple ligands on a protein,the ligands were correct initially (without explicit hydrogen ATOMS all ligands were processed by same method) but some ligand poses show additional hydrogen atom in the ligand output whereas some ligands did not show explicit hydrogen atoms.
  
  I also tried using two docking platforms autodock vina as well as QVina.
  
  I have uploaded the ligand output one with no issue and other with explicit hydrogens.
  
  [![Ligands pose output](https://i.sstatic.net/AjqCZd8J.jpg)](https://i.sstatic.net/AjqCZd8J.jpg)
  
  We received additional hydrogen along with ligands as you can see in second image and before docking the ligand is normal (image 1). So here is what we perform firstly we optimize the ligand structure using RDKit and apply the MMFF (Merck Molecular Force Field) for energy minimization. Subsequently, perform molecular docking using QVina to produce this output.
  
  Why did this happen and how do I solve this?
  
  **Tags:** protein-structure, docking, chimera, autodock
  
  > **Comments:**
  > **username_1**: Why is this question tagged with chimera?  
  > **username_0**: plz provide solution  
  > **username_1**: I don't know enough about the problem to be able to provide a good solution. I'm trying to help you improve your question, so that someone who *does* know about this domain can give a better answer.  
  > **username_2**: please provide at least two ligannds and describe the procedure that gave out two different kind of results  
  > **username_2**: cant you just feed the algho with ligand already contining explicit Hs provided by third party procedure ??  
  
  ---
  
  ## 0 answers
  
  