Re: [AMBER] Wrong bond types in Antechamber MOL2

From: Denis Schmidt <>
Date: Tue, 09 Dec 2014 11:08:22 +0100

Hi Hannes,

thanks for your swift reply!

Am 09.12.2014 10:30, schrieb Hannes Loeffler:
> 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?
I can't give you details about the imlementation of DOCK; it may even
rely on atom types only and thus work correctly, but that is speculative.
But independently of that, SYBYL bond types include not only single and
double bonds but also amide ("am") and aromatic/delocalized ("ar") bonds.
I assume, "ar" would be the "correct" bond type for the two bonds of a
carboxylate group.
>> 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
> matter.
I agree that the conversion to mol2 is based on a mapping table, so I'll
rephrase my question.
Might it be a better choice to map bond type "9" (delocalized) to bond
type "ar" (aromatic/delocalized) instead of mapping it to a single bond?
> Cheers,
> Hannes.

Best, Denis

D e n i s   S c h m i d t
Graduate Student
Pharmaceutical Chemistry . Philipps-University Marburg, Germany
Tel +49 6421 28 21351
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Received on Tue Dec 09 2014 - 02:30:02 PST
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