Hi Joe,
Yes, MCPB.py is capable to do such a task.
I checked Carvalho’s paper: https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.23287 <https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.23287?casa_token=lJic1xXbpWgAAAAA:uT9N6Pv-v1qBfOjHH8E_X9o1vhW09YORzLLstbfH61K4TGmUkL9x_rcepxT5rKJTcFbnz6xg9BfbFw>, and found they used the Seminario method to get bond/angle parameters and RESP algorithm to get charges. MCPB.py have these methods implemented as well. If you do not want to take efforts to re-parameterize the Fe4S4 parameters, you can just use Carvalho’s parameters for that. If you want to use Carvalho’s bond/angle parameters but want to use MCPB.py to derive the charges, I think it is fine as well.
Hope it helps,
Pengfei
> On Jan 14, 2020, at 11:51 PM, Baker, Joseph <bakerj.tcnj.edu> wrote:
>
> Hi Pengfei,
>
> I also have a need to simulate a protein with an Fe4S4 cluster in it. Is
> MCPB.py capable of such a task? In using the bond/angle parameters from the
> Carvalho paper did you rederive charges in your case for your specific
> system? Thanks for your advice.
>
> Kind regards,
> Joe
>
> ------
> Joseph Baker, PhD
> Associate Professor
> Department of Chemistry
> C212 Science Complex
> The College of New Jersey
> Ewing, NJ 08628
> Phone: (609) 771-3173
> Web: http://bakerj.pages.tcnj.edu/
> Pronouns: he/him/his
>
> Chair/Chair-elect (2019), Trenton Local Section of the ACS
> Chemistry Division Councilor (2018-2021), The Council on Undergraduate
> Research
>
>
>
> On Sat, Sep 7, 2019 at 6:03 PM Pengfei Li <ambermailpengfei.gmail.com>
> wrote:
>
>> Hello Jiawen,
>>
>> For generating parameters for a Fe-S cluster using MCPB.py, you should
>> treat each Fe or S atom as an independent residue in the PDB file, such as
>> (note that the residues after the Fe-S cluster need to have renumbered
>> residue numbers. For renumbering the residues, you can use the pdb4amber
>> program in AmberTools):
>>
>> HETATM 734 FE FE A1602 13.398 11.548 21.999 1.00 26.97
>> FE
>> HETATM 735 FE FE A1603 12.925 10.090 19.701 1.00 26.54
>> FE
>> HETATM 736 S S A1604 14.657 9.885 21.071 1.00 26.27
>> S
>> HETATM 737 S S A1605 11.681 11.837 20.546 1.00 27.47
>> S
>>
>> Or you can use the parameters for the Fe-S cluster(s) from this paper:
>> Carvalho, A. T.; Swart, M., Electronic Structure Investigation and
>> Parametrization of Biologically Relevant Iron–Sulfur Clusters. J. Chem.
>> Inf. Model. 2014, 54, 613-620.
>>
>> Hope it helps,
>> Pengfei
>>
>>> On Sep 3, 2019, at 12:11 AM, 崔佳文 <cui_jw17.sioc.ac.cn> wrote:
>>>
>>> Hello!
>>>
>>> I'm performing a molecular dynamics simulation of iron-sulfur protein
>> and having problems generating parameter documents using MCPB.py. I read
>> your tutorial on Internet.
>>>
>>> When I prepare the PDB and mol2 files for the non-standard residues, I
>> found it's difficult to generate files for sulfur in iron-sulfur cluster.
>> Could you please tell me how should I treat this kind of nonmetallic ions?
>> The attachment is my PDB file.
>>>
>>> Thanks for your time and consideration. I am looking forward to hearing
>> from you!
>>>
>>>
>>>
>>>
>>> Best regards,
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> ——————————
>>>
>>> Jiawen Cui
>>>
>>> (+86)17621824824
>>>
>>> Shanghai Institution of Organic Chemistry, Chinese Academy of
>> Science<1a70.pdb>_______________________________________________
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Received on Sat Jan 18 2020 - 17:00:02 PST
