AMBER Archive (2009)

Subject: Re: [AMBER] Antechamber ligand prep

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue Jan 27 2009 - 09:33:57 CST

On Tue, Jan 27, 2009, George Tzotzos wrote:
>
> 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.

Just remove the conect lines for now...we never test antechamber with
such records. Or, convert to mol2 as an input format.

...dac

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