You don't provide much information on how you set up and run your simulation.
However, your structure looks reasonable - I would expect it to be distorted from planarity due to steric repulsions.
All the best,
Andy
On Oct 14, 2010, at 4:43 AM, abc def wrote:
> 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,
> <Ligand-After simulation.pdb><Ligand-Before simulation.pdb>_______________________________________________
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--
Dr. Andreas W. Goetz
San Diego Supercomputer Center
Tel : +1-858-822-4771
Email: agoetz.sdsc.edu
Web : www.awgoetz.de
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Received on Thu Oct 14 2010 - 07:30:03 PDT
