[AMBER] MCPB.py with mixed valence di-iron system?

From: Gustavo Seabra <gustavo.seabra.gmail.com>
Date: Thu, 27 Feb 2020 17:11:06 -0500

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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Received on Thu Feb 27 2020 - 14:30:02 PST
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