On Tue, 9 Dec 2014 11:08:22 +0100
Denis Schmidt <denis.schmidt.staff.uni-marburg.de> wrote:
> 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 <denis.schmidt.staff.uni-marburg.de> 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.
That shouldn't be just speculation. How can you be sure the DOCK
interprets the ar type in a sensible way?
BTW, openbabel assigns the ar type to those two bonds but you may find
that chemoinformatic tools in general may fail in certain situations.
It's not a trivial problem after all and I would suggest to really know
what input a certain program needs and always check the output of some
tool.
Cheers,
Hannes.
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Received on Tue Dec 09 2014 - 03:00:02 PST
