Hi Patsch,
This paper maybe helpful as well: https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.23287 <https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.23287>.
BTW, MCPB.py can also help one to parameterize Fe-S clusters. Here are two examples about using MCPB.py to parameterize metal sites in metalloproteins: http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm>, http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm>.
Pengfei
> On Aug 27, 2021, at 7:33 AM, Gerald Monard <gerald.monard.gmail.com> wrote:
>
> Hello,
>
> If it can help, you will find in the supporting information of
> http://dx.doi.org/10.1002/prot.24991 some parameters and some leap input
> files for a protein iron-sulfer cluster.
> Good luck!
>
> Gerald.
>
>
> On Fri, Aug 27, 2021 at 9:09 PM David A Case <dacase.chem.rutgers.edu>
> wrote:
>
>> On Thu, Aug 26, 2021, Patsch David (patc) wrote:
>>>
>>> I am pretty new to MD and seriously stuck with parametrizing an
>> iron-sulfur
>>> cluster. I saw an old thread on this mailing list(which is why i
>>> subscribed) that suggested using the parameters described in this paper:
>>> https://doi.org/10.1021/ci400718m
>>>
>>> however, it is completely beyond me how to make use of that.
>>
>> You might write to the authors to get more information. As far as I can
>> see, the paper (and supporting information) only give bond stretching
>> parameters, with no information on angles or torsions. Partial charges are
>> provided, but Lennard-Jones information seems to be missing. The authors
>> might have Amber library and frcmod files available.
>>
>> You might also want to say what kind of iron-sulfur cluster you are trying
>> to model. That might prompt some more replies.
>>
>> ....dac
>>
>>
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Received on Mon Sep 06 2021 - 16:00:02 PDT
