AMBER Archive (2009)

Subject: Re: [AMBER] Antechamber Connectivity

From: George Tzotzos (
Date: Mon Jan 26 2009 - 12:23:58 CST

 Hi everybody,

I'm trying to run antechamber on a ligand pdb file (Hs and charges already added). The ligand is an unsaturated aliphatic aldehyde (13 carbon atoms).

Antechamber rejects the ligand on account of wrong connectivity

13 is not a valid atom id in CONECT 13 12 11 10

I have checked the connectivity and looks OK to me.

I'm attaching the ligand pdb with connectivities. Your help would be greatly appreciated. It seems to me a trivial problem but I'm really stuck at the moment.

Thanks in advance


  • application/octet-stream attachment: lig.pdb

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