Dear Amber users,
I am simulating a protein with non standard residue. I built the ligand structure using CASHE software and saved the structure as mol2 or pdb file. I used antechamber and gaff force field to get the necessary parameters. My question is how can I check the geometry of my ligand after calculations?
I used vmd and chimera, the structures look good but there is no way to make sure that double and single bonds are correct. However, when I used CASHE or Gaussian view to look at the pdb structure , each program gives me a structure with weired bonds different from each other and from the one I built and wanted. I even looked at the sustiva.pdb structure "tutorial4b" in gaussian view, it gives me disconnected molecule. The pdb structures don't have any information about the bond kind, So How do I figure out whether my calculations have the correct ligand structure or not?
Thank you,
Darine
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Received on Sat Oct 09 2010 - 13:30:03 PDT
