Dear Henry
The extra-point parameters for halogen bonding simulation can be find in
our original paper (Mahmoud A. A. Ibrahim, Molecular mechanical study of
halogen bonding in drug discovery, Journal of Computational Chemistry 2011,
32, 2564-2574).
Sincerely;
M. Ibrahim
On 23 September 2015 at 01:04, Thomas Cheatham <tec3.utah.edu> wrote:
>
>
> > After reading the papers about the positive extra-point approach in
the
> > AMBER general force field (GAFF) (*Ibrahim, J. Phys. Chem. B, 2012, 116,
> > 3659-3669*) and the polarizable ellipsoidal approach (*Liu et. al, JCC,
> > 2013, 34, 2032-2040*), we would like to try these force fields in our
free
> > energy calculation cases, if possible. However, we didn't find these
force
> > fields in the current AMBER 14 settings. Could anyone enlighten?
Thanks!
>
> That is true. If you carefully look at those papers, they talk about
> "AMBER compatible" force fields, not necessarily those *implemented* in
> AMBER. The first paper did the empirical calculations with a QM program
> and the second did not mention implementation details or code used. It
> may be possible to implement these in AMBER, but it will be challenging,
> especially as details in the papers are somewhat sparse. I would suggest
> contacting the authors.
>
> --tec3
>
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--
Mahmoud A. A. Ibrahim
Head of CompChem Lab, Chemistry Department,
Faculty of Science, Minia University, Minia 61519, Egypt.
Email: m.ibrahim.compchem.net
m.ibrahim.mu.edu.eg
Website: www.compchem.net
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Received on Wed Sep 23 2015 - 02:30:04 PDT
