Forum: Ligand optimization for docking
gravatar for madhu9ram
4.7 years ago by
Sri Lanka
madhu9ram0 wrote:

I'm confusing on ligand optimization . I have used gabedit software for this, Very first I have drew my compound after that I choose these option in gabedit 

- Set atom types,Molecular Mechanics(look for lower energy conformtion)

- MM gradient point optimization

- Minimization-Molecular dynamics conformational search-MD,gradients,MM  option for force fields 


After that I have saved my final optimized compound PDB format for chimera Auto-dock vina Docking

But when I see these compounds some compounds bonds breaking , only showing atoms. Not a proper structure as earlier inserted one . why is it? So please help me , Do I need to select any option here or Do I need to do mopac optimization for docking in chimera Autodockvina? 


Further, I did optimization in chemsketch software also  . I used Hex software for docking Sir. But I got better results from gabedit optimized structure (Followed above steps) rather than chemsetch optimization . 


Now I m confusing my optimization part. Those I followed steps are correct or not ..please help me

ligand optimization forum • 2.4k views
ADD COMMENTlink written 4.7 years ago by madhu9ram0

I think it is very hard to grasp what this question is about, I think you should include an example by posting an image or something reproducible. Also, your question looks similar to Ligand Structure Looks Different - After Docking

ADD REPLYlink written 4.7 years ago by Michael Dondrup46k
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