Hi,
The 12-6-4 will be in the next AMBER release, so you can access this technology once the new version is out. In the meantime we dug up the coordination numbers, ion-oxygen distances and hydration free energies for a range of M(III) species. If you have a water model that is your favorite we can focus on this model first using both the 12-6 model and the 12-6-4 for Fe(III). Once we have this in hand we can jump to the other water models to generate the full story.
Hope this helps,
Kennie
On Mar 7, 2014, at 11:07 AM, JPB <jpb.q4md-forcefieldtools.org> wrote:
> Hi Pengfei,
>
> I was not talking about building a topology with Fe2+,
> I don't really need help on this one.
>
> My point is to build upon an existing model
> of a bioinorganic complex containing Fe3+
> and improve it by using state of the art description
> of the LJ potential.
> Hence, I am planning to use the LJ potential you introduced in your 2014 JCTC.
> The problem is I do not have access to the version of
> the pmemd(?) program in which you implemented this new potential.
> So, to put it brief, it would be great, if we could collaborate on this one
> and you could give me the opportunity to access a version of pmemd
> working with the modified non-bonded potential.
> I also understood that you are currently developing the parameters
> for Fe3+ which are the ones I am interested in.
>
> Cheers.
> JPB.
>
>
>
> Pengfei Li <ambermailpengfei.gmail.com> a écrit :
>
>> Hi Jean-Paul,
>>
>> 2014-03-06 9:47 GMT-05:00 Jean-Paul Becker <jpb.q4md-forcefieldtools.org>:
>>
>>> Hi Pengfei,
>>>
>>> It will certainly not surprise you that one of my major concern is time.
>>> It seems that between the parametrization and the availability of
>>> the potential in Amber14, it can be within more than a couple of
>>> months from now.
>>> My dynamics are currently running with the 'old' parameters and I
>>> would have liked
>>> to have the opportunity to assess your development right away.
>>
>> I will be glad if you can send the parameters to me as soon as you get them.
>>>
>>
>> No problem. Since the parameters may be different for different water
>> models.
>> Can you tell me which kind of water model are you using in the simulation?
>> I can design that set of parameters with priority. I will send you the
>> parameters when
>> we get them.
>>
>>
>>> By the way, with your agreement, they can be a great addition to the RED
>>> DB.
>>>
>>
>> Yeah, go ahead. It has been published, feel free to add this into the RED
>> DB.
>>
>> Cheers.
>>> JPB.
>>>
>>
>> All the best,
>> Pengfei
>>
>>
>>>
>>>
>>>
>>> Pengfei Li <ambermailpengfei.gmail.com> a écrit :
>>>
>>>> Hi Jean-Peul,
>>>>
>>>> The 12-6-4 model has been added to Amber 14 as a new feature which will
>>> be
>>>> released in the coming April. For the Fe3+ ion, the 12-6-4
>>> parameterization
>>>> work is undergoing in our group. Since there are also other projects
>>>> undergoing, it may take some time for us to get it (and if you are
>>>> interested in, we can send you the parameter after we get it). Hope this
>>>> helps, if you have more questions or concerns, please tell me.
>>>>
>>>> All the best,
>>>> Pengfei
>>>>
>>>>
>>>>
>>>>
>>>> 2014-03-05 16:11 GMT-05:00 Jean-Paul Becker <
>>> jpb.q4md-forcefieldtools.org>:
>>>>
>>>>>
>>>>>
>>>>> ----- Message transféré de jean-paul.becker.u-picardie.fr -----
>>>>> Date : Wed, 05 Mar 2014 20:32:24 +0100
>>>>> De : Jean-Paul Becker <jean-paul.becker.u-picardie.fr>
>>>>> Objet : Re: [AMBER] non-bonded parameters for ferric iron and ferrous
>>>>> iron
>>>>> À : AMBER Mailing List <amber.ambermd.org>, Ken Merz <
>>>>> kmerz1.gmail.com>
>>>>> Cc : Pengfei Li <ldsoar1990.gmail.com>
>>>>>
>>>>> Hi Kennie,
>>>>>
>>>>> Thanks for the answer.
>>>>> Regarding the topology of the bonded model we took advantage of our
>>>>> RED server and especialy its new version written in Python.
>>>>> However, I would be very curions and interested to use your LJ params
>>>>> for trivalent cations (ferric iron) on our model and évaluate how they
>>>>> perform.
>>>>> Right now, I am not sure which way to proceed, I don't know how much
>>>>> it implies
>>>>> to use 12-6-4 model within Amber.
>>>>> Cheers.
>>>>> JPB
>>>>>
>>>>> Ken Merz <kmerz1.gmail.com> a écrit :
>>>>>
>>>>>> Hi,
>>>>>> We created LJ params for the ferrous iron, but not ferric
>>>>>> (http://pubs.acs.org/doi/abs/10.1021/ct400146w and
>>>>>>
>>>>>
>>> http://pubs.acs.org/doi/abs/10.1021/ct400751u?prevSearch=pengfei%2Bli&searchHistoryKey=
>>> ).
>>>>> We might be willing to create these for you if you are dissatisfied with
>>>>> what is out there. We can create a 12-6 or a 12-6-4 model depending on
>>> how
>>>>> you want to proceed. To create a bonded model for the coordination
>>>>> environment you can use MCPB. Good luck,
>>>>>> Kennie
>>>>>>
>>>>>> On Mar 4, 2014, at 12:08 PM, Jean-Paul Becker
>>>>>> <jpb.q4md-forcefieldtools.org> wrote:
>>>>>>
>>>>>>> Dear Amber users,
>>>>>>>
>>>>>>> I searched the bibbliography for non-bonded parameters for
>>>>>>> a five-coordinate ferric iron.
>>>>>>>
>>>>>>> There are the well known values coming from D.A. Giammona's PhD
>>>>>>> thesis (1.2 and 0.05)
>>>>>>> that were once in the Amber contrib but removed recently.
>>>>>>> These values are said to be appropriate for a six-coordinate iron
>>>>> though.
>>>>>>>
>>>>>>> In the supporting information of Shahrokh et al. (J. Comput. Chem.
>>>>>>> 33:119-133,2012)
>>>>>>> one can find three sets of non-bonded parameters either for ferrous
>>>>> iron or
>>>>>>> ferric iron in different environment:
>>>>>>> 1.8 0.01
>>>>>>> 1.3 0.002
>>>>>>> 1.3 0.01
>>>>>>> but reading the paper, the method used to derive these parameters
>>> does
>>>>>>> not appear clearly.
>>>>>>>
>>>>>>> In Shahrokh et al., a reference leads to Moore et al.
>>>>>>> (Biochemistry 49:9011-9019,1010) where one can read:
>>>>>>> "The van der Waals parameters for the heme iron atom were manually
>>>>>>> assigne Rii
>>>>>>> and epsii values of 1.3 and 0.01, respectively."...
>>>>>>>
>>>>>>> I am wondering where to look for published and trustworthy non-bonded
>>>>>>> parameteres suitable
>>>>>>> to ferric iron in a five-coordinate environment.
>>>>>>> My question is also more general and applies to ferrous and ferric
>>>>>>> iron in five-coodinate
>>>>>>> and six-coordinates environmants as well.
>>>>>>> Any suggestion would be deeply appreciated.
>>>>>>>
>>>>>>> Cheers.
>>>>>>> JPB.
>>>>>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>
>
>
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Kenneth M. Merz, Jr.
Director, Institute for Cyber Enabled Research (iCER)
Editor-in-Chief, Journal of Chemical Information and Modeling
Joseph Zichis Chair in Chemistry
Department of Chemistry
Department of Biochemistry and Molecular Biology
Michigan State University
578 S. Shaw Lane
East Lansing, MI 48824-1322
Phone: 517-355-9715 (Chemistry)
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iCER Help: https://contact.icer.msu.edu/contact
However, one should bear in mind that a macromolecular refinement against high resolution data is never finished, only abandoned.
George Sheldrick (2008), Acta Crystallogr. D64 112–122.
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Received on Fri Mar 07 2014 - 08:30:03 PST
