>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>
>>X-X-Sender: gmc.gx260.lcm3b.u-nancy.fr
>>To: amber.scripps.edu
>>Subject: Re: AMBER: manganese ion
>>MIME-Version: 1.0
>>X-Spam-Score: 0.00 () [Hold at 5.00] SPF(none,0)
>>X-Scanned-By: CanIt (www . roaringpenguin . com) on 137.131.200.30
>>X-Scanned-By: poincare.ciril.fr on 194.214.217.19
>>X-Bayes-Prob: 0.0001 (Score 0)
>>X-CanItPRO-Stream: majordomo (inherits from default)
>>X-Canit-Stats-ID: 30304242 - 88e4d8679568 (trained as not-spam)
>>X-Antispam-Training: Train as spam:
>>X-Antispam-Training: Train as non-spam:
>>X-Antispam-Training: Cancel training:
>>
>>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
>>
>>-----------------------------------------------------------------------
>>The AMBER Mail Reflector
>>To post, send mail to amber.scripps.edu
>>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Jul 11 2007 - 06:07:58 PDT
