Hi Jean-Paul,
I have started the project for parameterization of trivalent metal ions in
TIP3P water model. When I get the results, I will send you an email.
All the best,
Pengfei
2014-03-10 4:03 GMT-04:00 JPB <jpb.q4md-forcefieldtools.org>:
> 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
> >>>>
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> 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.
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Pengfei Li
Ph.D. Candidate
Merz Research Group
Department of Chemistry
Michigan State University
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Received on Thu Mar 13 2014 - 09:00:02 PDT
