[gmx-users] MD simulation of metalloprotein

[andrea spitaleri]

Hi,

we have determined the Mn2+ OPLSA sigma and epsilon parameters in 
http://onlinelibrary.wiley.com/doi/10.1002/anie.201202032/suppinfo 
following the procedure reported here 
http://pubs.acs.org/doi/abs/10.1021/jp064835t

hope it helps

and

On 28/04/2015 14:12, Justin Lemkul wrote:
>
>
> On 4/28/15 1:29 AM, Biplab Ghosh wrote:
>> Dear All,
>>
>> I am a beginner in MD and started with Gromacs. I would like to simulate
>> the dynamics of a homo-dimeric
>> protein containing  2 Mn atoms at the active site. I would appreciate 
>> any
>> sorts of help in this regards, e.g.,
>> please share your experience and/or relevant source in the web/published
>> literature.
>>
>> Which force-filed would be appropriate? How can I take care of the metal
>> ions?
>>
>
> We've had reasonably good success with AMBER Mn2+ in concert with 
> distance restraints on the ligating residues:
>
> http://www.pharmacy.manchester.ac.uk/bryce/amber
>
> -Justin
>

-- 
Andrea Spitaleri PhD
D3 - Drug Discovery & Development
Istituto Italiano di Tecnologia
Via Morego, 30 16163 Genova
cell: +39 3485188790
http://www.iit.it/en/d3-people/andrea-spitaleri.html
ORCID: http://orcid.org/0000-0003-3012-3557