Brian and
Yang,
Thank you
for your help!
All the
best,
Filip
________________________________
From: "Yang, Yue" <yang.qtp.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Cc: filip fratev <filipfratev.yahoo.com>
Sent: Tuesday, April 24, 2012 2:26 AM
Subject: Re: [AMBER] QM/MM ATP-Mg2+ system
Hello,
I'm pretty sure Mg2+ is included in the set of SCC-DFTB parameters that Brian mentioned.
I have used that set of parameters to study several prenyltransferase catalysis when I was
a graduate student with Dr. Kenneth Merz. It's working well (or great), but Mg2+ might need
some special care - in our case, keeping Mg2+ in MM and including it in QM don't make a
lot differences so we keep in MM so 20 more atoms can also be kept in MM. But I'm pretty
sure it's there and working. If you need any related reference, just search Merz group's
recent publications.
In addition, if you can't find that parameter from dftb.org, write directly to Dr. Qiang Cui at
Wisconsin. He's very friendly and definitely an expert at this.
Best,
Yue
On Apr 23, 2012, at 9:03 AM, Brian Radak wrote:
> 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
> catalysis.
>
> 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*,
> 1.
>
> 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*,
> 2067.
> DFTB3 - Gaus, *et al. J. Chem. Theory Comput. **2011*, *7*, 931.
>
> (Apparently J. Chem. Theory Comput. is a popular place for these things).
>
> Regards,
> Brian
>
> On Sun, Apr 22, 2012 at 6:55 PM, filip fratev <filipfratev.yahoo.com> 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 <filipfratev.yahoo.com>
>> To: filip fratev <filipfratev.yahoo.com>; AMBER Mailing List <
>> amber.ambermd.org>
>> 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 <filipfratev.yahoo.com>
>> To: AMBER Mailing List <amber.ambermd.org>
>> Cc: Andreas Goetz <agoetz.sdsc.edu>
>> 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 <agoetz.sdsc.edu>
>> To: AMBER Mailing List <amber.ambermd.org>
>> Cc: filip fratev <filipfratev.yahoo.com>
>> 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: agoetz.sdsc.edu
>> Web : www.awgoetz.de
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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
> Proteomics Room 308
> Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> Department of Chemistry : Piscataway, NJ
> 08854-8066
> radak004.umn.edu :
> radakb.biomaps.rutgers.edu
> ====================================================================
> Sorry for the multiple e-mail addresses, just use the institute appropriate
> address.
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Received on Tue Apr 24 2012 - 14:00:04 PDT
