Hi Kennie and Pengfei,
My favorite water model is tip3p.
It would be nice if you could start with this one.
Thanks for your consideration.
Cheers.
JPB.
Ken Merz <kmerz1.gmail.com> a écrit :
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>
> 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)
> 517-884-2540 (iCER)
> 517-353-7248 (Fax)
> Cell: 814-360-0376
>
> e-mail: kmerz1.gmail.com
> http://www.merzgroup.org/
> https://icer.msu.edu
> 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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>
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Received on Mon Mar 10 2014 - 01:30:03 PDT
