Re: [AMBER] QM/MM ATP-Mg2+ system

From: Brian Radak <>
Date: Mon, 23 Apr 2012 12:03:39 -0400

Hi Filip,

Unfortunately I don't believe that is a question with a definitive answer.
I would say your 2 best options are probably either AM1/d-PhoT (the default
for "AM1D") or MNDO/d. Another option might be SCC-DFTB.

AM1/d-PhoT was only specifically parameterized for phosphoryl (and some
proton) transfer. The AM1/d Mg parameters by Imhof, *et al.* are also
defaults under "AM1D", but were not parameterized with the same O and H
parameters as AM1/d-PhoT. I would therefore be hesitant to claim that
binding affinities are well reproduced by that combination. Our group has,
however, had success with that combination in the past for ribozyme

MNDO/d is less specialized than AM1/d-PhoT and I know it actually does
pretty well on a lot of things, but I'm not familiar with any recent
literature discussing it's use.

There is, I believe, an SCC-DFTB set for P, S, O, C, N, and H. Mg might be
possible also, but I don't remember. There was some work a while ago on a
partial 3rd order extension of SCC-DFTB that included a specialized set for
phosphate hydrolysis, but I don't know how widely it was used. It has
since been effectively replaced by a full 3rd order extension, but that is
not implemented in SQM to my knowledge. I don't know if there are any
solid plans to make that addition, as DFTB3 (as it's called) is still a
rather nascent method. Maybe Adrian Roitberg or Gustavo Seabra would have
a comment on that front, but I wouldn't pretend to speak for them.

Some papers you might consider:

AM1/d-PhoT - Nam, *et al.* *J. Chem. Theory Comput.* *2007*, *3*, 486.
Mg + AM1/d - Imhof, *et al. J. Chem. Theory Comput.** 2006**, 2*, 1050.
Mg related catalysis - Wong, *et al. J. Chem. Theory Comput.* *2011*, *7*,

SCC-DFTB + 3rd order - Yang, *et al. J. Phys. Chem. A* *2007*, *111*, 10861.
phosphate hydrolysis - Yang, *et al. J. Chem. Theory Comput.* *2008*, *4*,
DFTB3 - Gaus, *et al. J. Chem. Theory Comput. **2011*, *7*, 931.

(Apparently J. Chem. Theory Comput. is a popular place for these things).


On Sun, Apr 22, 2012 at 6:55 PM, filip fratev <> wrote:

> Hi all,
> I'd like to ask you what semi-empirical method in Amber will best fit for
> ATP-Mg2+ system and what is the best way, in your opinion, to describe the
> energy difference of ATP-Mg2+ binding if some mutations are present in the
> ATP binding pocket?
> All the best,
> Filip
> ________________________________
> From: filip fratev <>
> To: filip fratev <>; AMBER Mailing List <
> Sent: Saturday, April 21, 2012 6:35 AM
> Subject: Re: [AMBER] AMBER12 QM/MM: is d-orbital code going to be
> parallelized?
> Hi,
> I made an additional test with larger (more realistic) QM region.
> The QM region consist of 164 atoms (ATP,Mg2+ and several Myosin
> residues);6-31g/rhf; 3 minimization steps:
> TeraChem 1GPU=231.65sec; 2GPU's=129.1sec (1.8x, but will be around 2x
> after 100 steps)
> Gaussian 4 cores .4.6Ghz= 1321.2sec;
> Thus we have 10.2x gain in performance for that system and the
> Amber-TeraChem link works well. I run only 3 steps and if we run 100 the
> speed up will be likely 15x. I did mistake in first test and now the
> results between TeraChem and Gaussian are very similar.
> Hope that this will help to those that interest in QM/MM simulations with
> Amber and TeraChem!
> All the best,
> Filip
> ________________________________
> From: filip fratev <>
> To: AMBER Mailing List <>
> Cc: Andreas Goetz <>
> Sent: Friday, April 20, 2012 8:30 AM
> Subject: Re: [AMBER] AMBER12 QM/MM: is d-orbital code going to be
> parallelized?
> Dear Prof. Case and Andreas,
> Thank you for your responses!
> I use the last TeraChem version - 1.5.
> According to Amber 12 manual there is no limitations, as such for GAMMES,
> for
> electronic embedding in TeraChem. Are you sure that with this version it is
> possible only mechanical embedding or I should I ask Petachem developers
> about
> that?
> I performed some tests using TeraChem and
> Gaussian as external programs to assess mainly the GPU speed up by
> TeraChem. I
> used two GTX580 3GB cards and 2600K.4.6Ghz CPU. Some results and
> questions:
> 1) Indeed all Amber tests passed.
> 2) Secondly I tested the example from Tutorial
> A2. Both programs work well with Amber link and gave very similar results
> using
> various parameters. In this test (only 12 QM atoms) Gaussian was faster
> than
> TeraChem (TC) for minimization. In the case of MD simulation I observed
> only
> 20% boost in the performance using TC. Moreover, TC was faster with one GPU
> instead of two (30% slower with 2 GPU's). This is likely due to the small
> system size. In fact using Gaussian I was not able to achieve some good
> CPU-core scale too.
> 3) Further I performed some more realistic tests
> using Myosin protein (MM) + ATP-Mg2+ (QM). The system is around 116K atoms
> solvated. Here TeraChem had a clear advantage but not exactly what I
> expected. During
> the 20 steps minimization TC was 4.75x faster than Gaussian (all cores) and
> during MD 4.3x. It is indeed impressive because for only 20 steps MD (it
> was
> 6-31G, but I do not remember b3lyp or something else) it took 705sec using
> Gaussian
> and only 163sec by TeraChem; 4,9ps vs 21.2ps/day. Here again the GPU scale
> is
> the main problem - the second GPU adds only 20% speed up. If I use only
> TeraChem for optimization it is 100%, thus one can expect around 8 x
> speeds up.
> What could be the problem? The software link or
> something else?
> I tested (not only now) the GPU speed up when
> use only TeraChem for optimization or just SP and it is exactly 2x for two
> GPU's, doesn't matter for 30 or 150 atoms. What are your advices and in
> general
> is it possible to be improved GPU speed up for the Amber-TeraChem
> combination?
> I am not expert in QM/MM calculations that's
> why would like to ask you what semi-empirical method in Amber will best
> fit for
> ATP-Mg2+ system and what is the best way, in your opinion, to describe the
> energy difference of ATP-Mg2+ binding if
> mutations are present in the ATP binding pocket?
> All the best,
> Filip
> ________________________________
> From: Andreas Goetz <>
> To: AMBER Mailing List <>
> Cc: filip fratev <>
> Sent: Thursday, April 19, 2012 10:50 PM
> Subject: Re: [AMBER] AMBER12 QM/MM: is d-orbital code going to be
> parallelized?
> On Apr 16, 2012, at 1:08 PM, David A Case wrote:
> > On Mon, Apr 16, 2012, filip fratev wrote:
> >
> >> I'd like to extend the question. According to
> >> the Amber 12 manual it is possible to perform QM/MM using TeraChem
> software
> >> (Cuda software). However, developers of the TeraChem ensured me that
> this not
> >> possible at the moment and probably will be possible in June.
> >
> > What happens when you try such calculations? In particular, do the
> TeraChem
> > test calculations work? (See, e.g.
> amber12/test/qmmm_EXTERN/QMMM_MD_TeraChem).
> >
> >> Thus, which programs are available at the
> >> moment for QM/MM calculations?
> >
> > Please see Section 3.7 of the Amber12 Reference Manual.
> >
> > ....dac
> For electronic embedding you need a TeraChem version that supports
> external point charge electric fields. You can try mechanical embedding if
> this fits your needs. This should work also with earlier versions of
> TeraChem. Check if following test works:
> $AMBERHOME/test/qmmm_EXTERN/QMMM_MD_TeraChem/Run.nma-spcfw-15.hf_sto-3g.MechEm
> Be aware that I have not extensively tested mechanical embedding.
> If you are using the interface to external QM programs, any feedback is
> appreciated.
> All the best,
> Andy
> --
> Dr. Andreas W. Goetz
> Assistant Project Scientist
> San Diego Supercomputer Center
> Tel : +1-858-822-4771
> Email:
> Web :
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================================ Current Address =======================
 Brian Radak                                             :     BioMaPS
Institute for Quantitative Biology
 PhD candidate - York Research Group       :     Rutgers, The State
University of New Jersey
 University of Minnesota - Twin Cities         :     Center for Integrative
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Received on Mon Apr 23 2012 - 09:30:02 PDT
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