AMBER Archive (2009)

Subject: Re: [AMBER] Antechamber Connectivity

From: David Watson (dewatson_at_olemiss.edu)
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).
>
[snip]
>
> 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
error:
*** 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.
[snip] 

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

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