AMBER Archive (2009)

Subject: Re: [AMBER] Antechamber ligand prep

From: George Tzotzos (
Date: Tue Jan 27 2009 - 10:44:06 CST

Hi David,

Just for information. Running antechamber after conversion of the ligand.pdb to mol2 format produces no complaints.

Given the fact that David Watson was able to run the pdb file in AMBER 9 it may be a problem of v.10. However, I thought that antechamber run independently of AMBER. Am I wrong?

Cheers and thanks again for the help. You may wish to see if this is a bug or a real 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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