David,
I don't have enough experience with the force field code in OpenBabel to be a
reliable source of information but I didn't find any calls of the
IsHbondAcceptor() function outside of atom.cc.
I would expect any force field to type the atoms basing on specific patterns
more than atomic properties, but, if I'm wrong, testing any force field should
show if there are problems.
Thanks,
S
(I've filled in the subject that I missed in the first submission)
--
Stefano Forli, PhD
Assistant Professor of Integrative
Structural and Computational Biology,
Molecular Graphics Laboratory
Dept. of Integrative Structural
and Computational Biology, MB-112F
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037-1000, USA.
tel: +1 (858)784-2055
fax: +1 (858)784-2860
email: fo...@scripps.edu
http://www.scripps.edu/~forli/
________________________________________
From: David van der Spoel [sp...@xray.bmc.uu.se]
Sent: Tuesday, December 29, 2015 2:04 PM
To: openbabel-devel
Subject: Re: [OpenBabel-Devel] (no subject)
On 29/12/15 23:00, Stefano Forli wrote:
> Hi,
> aiming at the 2.4 release, I've proposed a patch for the function
> OBAtom::IsHbondAcceptor(), which is a bit more fine-grained than the current
> one, which is essentially based only on the element, see here:
>
> https://github.com/openbabel/openbabel/pull/244
>
> The goal was to provide results more accurate for small organic molecules
> (i.e., drug-like, fragments, etc...) so my tests were mainly based on
> molecules like these.
> Geoff suggested to check also for possible effects of this change on the
> force field typing (which, *hopefully* should be non-existent) so it would be
> great if anybody with a bit more experience on the matter could take a look.
>
> Thanks!
>
> S
>
*any* force field typing, or a specific one?
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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