Re: [AMBER] problems on amoeba force filed implemented in amber

From: Brian Radak <>
Date: Wed, 15 Jul 2015 11:53:17 -0500

I have only seen a few QM/MM calculations utilizing polarizeable MM and
usually with Drude oscillators instead of AMOEBA. Both of these have
been recently attempted in ChemShell, although I only know this because
a colleague of mine recently finished his PhD on the matter. So based on
this knowledge:

1) you are better off trying for a Drude model
2) it will be challenging to run MD, but optimizations are likely possible
3) you will have to do some begging around the ChemShell community to
get some pre-release code, if they are so inclined


On 07/14/2015 07:11 AM, Jason Swails wrote:
> On Tue, Jul 14, 2015 at 5:35 AM, fjliu <> wrote:
>> Thanks for your reply. So I can not do the QM/MM calculation with the
>> amoeba water. Can you give me some advice about which program maybe I
>> can use for do this ?
> ​I believe there may be some development of this feature going on in some
> version of Tinker somewhere (not the official version, though). But for
> programs that do this that can be easily downloaded and run, I'm not aware
> of any.
> QM/MM simulations where MM includes explicit polarization (and in the case
> of the Amoeba force field, permanent point-dipoles and quadrupoles) are far
> less mature than the (much easier) monopole-only, fixed-charge force
> fields.​ The best hit I saw from Google was this:
> (but I didn't look
> very hard).
> ​​
>> ​​
>> Will you write this part in future? Thank you!
> ​Me, no. I won't say it will never happen, but it certainly won't in the
> immediate future (i.e., the next couple of years at least).
> HTH,
> Jason

Brian Radak
Postdoctoral Scholar
Gordon Center for Integrative Science, W323A
Department of Biochemistry & Molecular Biology
University of Chicago
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812
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Received on Wed Jul 15 2015 - 10:00:03 PDT
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