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
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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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Jan 14 2020 - 21:00:01 PST
