Dear Thomas and Mahmoud,
Thank you for your comments. I will look into it.
Best,
Henry
On Wed, Sep 23, 2015 at 4:00 AM, Mahmoud A. A. Ibrahim <
m.ibrahim.compchem.net> wrote:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> --
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Pin-Chih Su (Henry Su)
Ph.D.
Center for Pharmaceutical Biotechnology (MC 870)
College of Pharmacy, University of Illinois at Chicago
900 South Ashland Avenue, Room 1052
Chicago, IL 60607-7173
office 312-996-5388
fax 312-413-9303
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Received on Wed Oct 28 2015 - 23:30:03 PDT
