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.
> >> >>
>
>
>
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--
Pengfei Li
Ph.D. Candidate
Merz Research Group
Department of Chemistry
Michigan State University
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Received on Thu Mar 06 2014 - 14:30:03 PST
