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 Sep 07 2019 - 15:30:02 PDT
