Hi Neetu,
in my situation the Mn2+ is connected both to amino acid both to DNA and i'm
testing the parameter that suggest me Guillermo Mulliert if you have read his
answer. If you don't have i'll forward you.
If you think that the approximation of your force field is strong i suggest to
do that : take your system MN2+ plus the two or more residues complexes with
that ion and cut all the other residues in a protein. make a DFT calculation of
that little system and then you can understand what's the minimum conformation
of your ion-resiudes complex and extrapolate the new charge.
I needn't do that work because i'm not interested to value energy but only shape
recognition and the parameter of Mn2+ find in the amber website are ok for me.
For any other suggestion i'm everytime available
Davide
>From: neetu.imtech.res.in
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>Date: Wed, 11 Jul 2007 09:33:54 +0530 (IST)
>Subject: Re: AMBER: manganese ion
>To: amber.scripps.edu
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>>Dear Davide,
>Some time back i also put the same problem in the forum. In my case,
>manganese ions are coordinated to four different amino acid residues of
>the protein. Amber demands force constants for different bonds, angles and
>dihedral angles before preparing topology and parameter files. I am
>struggling to get those parameters.
> I want to know whether Mn in your protein also interacts to some residues
>and if yes then how you have generated those parameters for manganese.
>Regards,
>Neetu Saxena,
>Research scholar,
>Bioinformatics Division,
>Institute of Microbial Technology,
>Chandigarh,
>INDIA.
>
>
> Hi Guillermo,
>> Thank you for the advise, it's what i was looking for!
>>
>> Davide
>>
>>
>>
>>>Date: Tue, 10 Jul 2007 10:39:40 +0200 (CEST)
>>>From: Guillermo Mulliert Carlín <Guillermo.Mulliert.lcm3b.uhp-nancy.fr>
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>>>To: amber.scripps.edu
>>>Subject: Re: AMBER: manganese ion
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>>>
>>>Hello,
>>>
>>>On Mon, 9 Jul 2007, Davide Moiani wrote:
>>>
>>>|> Hi everybody,
>>>|> I need to simulate a protein with two manganese ions , before to make
>>> a
>> library
>>>|> i ask if someone had simulated before and could send me a library or
>>> the
>>>|> coefficents to put in the parm99.dat.
>>>
>>>
>>> Have you take a look at
>>> http://amber.scripps.edu/
>>> Contributed parameters database, maintained by Richard Bryce at the
>> University of Manchester
>>>
>>>under Ions there are parameters for Mn(2+)
>>>
>>>
>>> Hope this help
>>>
>>> Guillermo Mulliert
>>>
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Received on Sun Jul 15 2007 - 06:07:12 PDT
