I think the problem is with the small-molecule ligand (CTZ) in binding pocket of the protein complex I'm trying to use.
Originally, there were too many bonds to each atom in the CTZ molecule. I used the SMILE software followed by REDS to get the right bond lengths and thus make it so each atom had the proper bond lengths and corrersponding # of Bonds (pdb file attached: (CTZ05.pdb). I then used antechamber to make the param and crd files. I followed the antechamber amber tutorial for this.
The problem now appears to be the complex. The CTZ molecule in the binding pocket has too many bonds to it and this is probably causing the problem (attached pdb 2psj_ctz_compex...pdb). I originally got the complex from a molgro file in the mol2 format.
I can't put the protein/ligand complex through SMILES again.
How can I fix this problem so that the ligand in the complex doesn't have the bonding problem?
Thanks,
Chris
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- application/octet-stream attachment: CTZ05.pdb
Received on Wed May 09 2012 - 08:30:03 PDT
