----- 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.
>>
>> --
>> Jean-Paul Becker
>> Equipe THERA
>> Laboratoire des Glucides
>> FRE 3517
>> 1 rue des Louvels
>> 80036 Amiens Cedex
>> France
>>
>>
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Received on Wed Mar 05 2014 - 13:30:02 PST
