AMBER Archive (2009)

Subject: Re: [AMBER] Antechamber ligand prep

From: George Tzotzos (
Date: Tue Jan 27 2009 - 09:43:19 CST

Once again thanks. I'll try mol2 and see what happens.

In the meantime I tried as per David Watson's suggestion (in Amber 10).

I get: antechamber -i ~/Desktop/test/new.pdb -fi pdb -o ~/Desktop/test/new.prepin -fo prepi -s 2
1 is not a valid atom id in CONECT 1 2 3 4

Is it possible it is an Amber 10 problem?


On Tuesday, January 27, 2009, at 04:33PM, "David A. Case" <> wrote:
>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.
>AMBER mailing list

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