[AMBER] Issue regarding buckling of planar ligand during simulations

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From: abc def <biotechabc.gmail.com>
Date: Thu, 14 Oct 2010 17:13:31 +0530

Hi,

I was trying to do simulation on a ligand molecule having planar structure.
And I used antechamber gaff parameters for my ligand. But I found that my
structure after simulation is no longer planar. It appears to be slightly
buckled up. Can you tell me what am I doing wrong? Does the gaff parameter
work for planar ligand molecules?

I have attached the structures both before and after running simulation.

Please let me know where I am going wrong.

Thanks in anticipation,

Regards,

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chemical/x-pdb attachment: Ligand-After_simulation.pdb

chemical/x-pdb attachment: Ligand-Before_simulation.pdb

Received on Thu Oct 14 2010 - 05:00:05 PDT