Dear Gustavo Seabra,
I started some simulations with Fe (III) -Zn (II) system using MCPB.py for
parameterization. Work in progress.
Perhaps the steps to follow if I have not forgotten anything needed before,
can help to evolve. Let's go and see your results.
Let me know if you were successful in the steps if it is convenient.
Fe(III)-Zn(II)
Input file for steps with MCPB.py: 2QFR.in
__________________________________________________________
original_pdb FE-ZN-A-OHM.pdb
group_name 2QFR
cut_off 2.8
ion_ids 6812
ion_ids 6813
ion_mol2files FE.mol2
ion_mol2files ZN.mol2
naa_mol2files OHM.mol2
frcmod_files OHM.frcmod
___________________________________________________________
For the first steps, two PDB files are created, one for each metal. Next,
obtain the pre-mol2 files that are edited with the
charge data for each metal and the type of atom changed
in the pre-mol2 file
Following these steps, see if you can get to the next step which is to get
the files to run the calculations using Gaussian, for example.
Having reached this point successfully, we will proceed to the next steps. See
that as in your case the two metals are the same
(FE1 and FE2 - should follow as an example for Zn-Zn).
___________________________________________________
ZN.pdb
ATOM 6813 ZN ZN 426 -0.051 -3.602 -10.842 1.00 0.00
____________________________________________________________
ZN_pre.mol2
.<TRIPOS>MOLECULE
ZN
1 0 1 0 0
SMALL
No Charge or Current Charge
.<TRIPOS>ATOM
1 ZN -0.0510 -3.6020 -10.8420 LP 426 ZN 0.000000
.<TRIPOS>BOND
.<TRIPOS>SUBSTRUCTURE
1 ZN 1 TEMP 0 **** **** 0 ROOT
_______________________________________________________________
ZN.mol2
.<TRIPOS>MOLECULE
ZN
1 0 1 0 0
SMALL
No Charge or Current Charge
.<TRIPOS>ATOM
1 ZN -0.0510 -3.6020 -10.8420 ZN 426 ZN 2.000000
.<TRIPOS>BOND
.<TRIPOS>SUBSTRUCTURE
1 ZN 1 TEMP 0 **** **** 0 ROOT
__________________________________________________________________
FE.pdb
ATOM 6812 FE FE 425 -2.313 -5.451 -9.918 1.00 0.00
____________________________________________________________________-
FE_pre.mol2
.<TRIPOS>MOLECULE
FE
1 0 1 0 0
SMALL
No Charge or Current Charge
.<TRIPOS>ATOM
1 FE -2.3130 -5.4510 -9.9180 DU 425 FE 0.000000
.<TRIPOS>BOND
.<TRIPOS>SUBSTRUCTURE
1 FE 1 TEMP 0 **** **** 0 ROOT
______________________________________________________________________
FE.mol2
.<TRIPOS>MOLECULE
FE
1 0 1 0 0
SMALL
No Charge or Current Charge
.<TRIPOS>ATOM
1 FE -2.3130 -5.4510 -9.9180 FE 425 FE 3.000000
.<TRIPOS>BOND
.<TRIPOS>SUBSTRUCTURE
1 FE 1 TEMP 0 **** **** 0 ROOT
____________________________________________________________________
Dr. Marcelo Andrade Chagas,
http://lattes.cnpq.br/7024808363863350
*eCsMo**Lab**: Laboratório de Estudos Computacionais em Sistemas
Moleculares*
Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
*
http://lqcmm.qui.ufmg.br/
Departamento de Química, ICEx, Universidade Federal de Minas Gerais
31270-901, Pampulha, Belo Horizonte, MG, Brazil.
Tel:(31)3409-5776
Gustavo Seabra <gustavo.seabra.gmail.com> escreveu no dia quinta,
27/02/2020 à(s) 19:11:
> Hi MCPB experts,
>
> I wonder if it is possible to run MCPB.py for a system with 2 Fe ions with
> different valences.
>
> I have this system with 2Fe-2S bound to a ligand. In the first step of
> MCPB.py, if I write both Fe ions as being the same kind, like:
>
> HETATM 7756 FE FE B 529 42.058 -18.411 -9.563 1.00 0.00
> FE2+
> HETATM 7757 FE FE B 530 41.201 -20.383 -8.098 1.00 0.00
> FE2+
> HETATM 7758 SFE SFE B 531 42.340 -18.690 -7.288 1.00 0.00
> S2-
> HETATM 7759 SFE SFE B 532 40.569 -19.994 -10.292 1.00 0.00
> S2-
>
> and the simple mol2 file below:
>
> .<TRIPOS>MOLECULE
> FE
> 1 0 1 0 0
> SMALL
> No Charge or Current Charge
>
> .<TRIPOS>ATOM
> 1 FE 42.0580 -18.4110 -9.5630 FE 530 FE
> 2.000000
> .<TRIPOS>BOND
> .<TRIPOS>SUBSTRUCTURE
> 1 FE 1 TEMP 0 **** **** 0 ROOT
>
> MCPB.py works fine to generate the files for the Gaussian calculation.
> However, this only works for me if both Fe ions are in the same oxidation
> state.
>
> I would like to simulate the II-III state. For that, I'd need the two Fe
> ions to have different residue names, say FE2 and FE3. However, if the
> residue name doesn't match the atom name, MCPB.py exits with an error. For
> example, I have tried using (notice that the difference is only on the
> residue numbers):
>
> HETATM 7756 FE FE2 B 529 42.058 -18.411 -9.563 1.00 0.00
> FE2+
> HETATM 7757 FE FE2 B 530 41.201 -20.383 -8.098 1.00 0.00
> FE2+
> HETATM 7758 SFE SFE B 531 42.340 -18.690 -7.288 1.00 0.00
> S2-
> HETATM 7759 SFE SFE B 532 40.569 -19.994 -10.292 1.00 0.00
> S2-
>
> and the mol2 file:
>
> .<TRIPOS>MOLECULE
> FE2
> 1 0 1 0 0
> SMALL
> No Charge or Current Charge
>
> .<TRIPOS>ATOM
> 1 FE 42.0580 -18.4110 -9.5630 FE 530 FE2
> 2.000000
> .<TRIPOS>BOND
> .<TRIPOS>SUBSTRUCTURE
> 1 FE2 1 TEMP 0 **** **** 0 ROOT
>
> but then MCPB.py crashes with the error:
>
> $ MCPB.py -i mcpb.in -s 1
> [...]
> Totally there are 88 atoms in the large model.
> Totally there are 401 electrons in the large model.
> Traceback (most recent call last):
> File "/opt/amber/amber18/bin/MCPB.py", line 644, in <module>
> addred, lgchg, lgspin)
> File
>
> "/opt/amber/amber18/lib/python3.7/site-packages/pymsmt/mcpb/gene_model_files.py",
> line 1910, in gene_model_files
> ionids, chargedict, lgchg, lgspin, outf, watermodel, largeopt, sqmopt)
> File
>
> "/opt/amber/amber18/lib/python3.7/site-packages/pymsmt/mcpb/gene_model_files.py",
> line 1604, in build_large_model
> chargedict, IonLJParaDict, largeopt)
> File
> "/opt/amber/amber18/lib/python3.7/site-packages/pymsmt/mol/gauio.py", line
> 286, in write_gau_mkf
> chg = int(round(chargedict[ionname], 0))
> KeyError: 'FE'
>
>
> I have tried different combinations of the atom/residue names, but in every
> case MCPB.py only seems to work if the atom AND residue name match, AND are
> both "FE". Any change seems to lead to a crash of some kind. ( I have
> attached the full output from MCPB.py here).
>
> So, my question again is, is it possible to use MCPB.py for a mixed state
> system like this one? If so, what am I doing wrong here? If not, is there
> another way?
>
> Thank you so much!
> --
> Gustavo Seabra.
> _______________________________________________
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>
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Received on Thu Feb 27 2020 - 18:00:02 PST
