Re: [AMBER] Wrong bond types in Antechamber MOL2

From: Hannes Loeffler <>
Date: Tue, 9 Dec 2014 09:30:11 +0000

On Mon, 8 Dec 2014 16:21:11 +0100
Denis Schmidt <> wrote:

> I'm using Antechamber (AmberTools 14 including latest updates) as
> part of a ligand preparation process required by Dock 3.7.
> It's role is to convert mol2 input to mol2 output and setting correct
> SYBYL atom types.
> I noticed that bond types were incorrectly set in the output mol2,
> however they look correct in the intermediate AC file.

In what sense is this incorrect? SYBYL apparently knows only
about single and double bonds for this problem which, however, from a
chemical point of few are not right. I am not familiar with DOCK but
why does it rely on bond types and how does it ensure that both
bonds/oxygen atoms are equivalent?

> Note that atoms 3,4 and 5 together form a carboxylate group. In the
> final output mol2 the bonds 3-4 and 3-5 are single bonds.
> However, the intermediate ANTECHAMBER_*.AC files reveal that the atom
> types (C.2 for atom 3 and O.co2 for atoms 4 and 5) and bond types
> (type 9, delocalized) are correctly set.
> This seems to be a problem of antechamber when converting AC to mol2.

Antechamber obviously perceives this functional group right. But I
suspect it doesn't have any special code, besides a one-to-one
mapping/table, that would find "appropriate" translations into other
bond type systems in more complex situations where functional groups

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Received on Tue Dec 09 2014 - 02:00:02 PST
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