AMBER Archive (2009)

Subject: Re: [AMBER] Antechamber Connectivity

From: David Watson (
Date: Mon Jan 26 2009 - 13:59:58 CST

On Jan 26, 2009, at 12:23 PM, George Tzotzos wrote:

> 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).
> I have checked the connectivity and looks OK to me.

When opened with PyMol, Swisspdb, etc. this molecule appears fine.
But when I try to convert it to another molecule with babel, I get an
*** Open Babel Error in ReadMolecule
   ERROR: not a valid PDB file

You might want to double check that the pdb actually does follow pdb
file format guidelines.

David Watson  Graduate Student  Medicinal Chemistry  425 Faser Hall  
 University MS  38677  1.662.915.1663

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