AMBER Archive (2009)

Subject: Re: [AMBER] Antechamber ligand prep

From: George Tzotzos (
Date: Tue Jan 27 2009 - 09:24:30 CST

 Hi David and David

Many thanks for the suggestion today and yesterday. I did try almost everything. I prepared de nove the ligand in Chimera. I'm attaching the file. I don't see anything wrong with connectivities or formating. Antechamber still refuses to accept the connectivity "1 is not a valid atom id in CONECT 1 2 3 4". I'm attaching the new ligand file in case you can see something that I miss.

Thanks again for your help


On Tuesday, January 27, 2009, at 03:59PM, "David A. Case" <> wrote:
>On Tue, Jan 27, 2009, George Tzotzos wrote:
>> 1. When I remove the CONECT lines and get warnings about duplicate
>> atoms, ARE THESE WARNINGS IMPORTANT or can I live with these?
>These are important, and should be fixed. Antechamber has some ability
>to automatically rename atoms to have unique names, but I don't think
>you should rely on it.
>AMBER mailing list

  • application/octet-stream attachment: new.pdb

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