Hi Ralph,
The error message you are getting is because MCPB doesn’t recognize “FE2” as the name for any metal ion. The below prior conversation on the ListServe shows how you need to differently setup the PDB file for an iron-sulfur cluster. Hope this helps!
http://archive.ambermd.org/202001/0215.html
Best,
Matthew
> On Dec 23, 2023, at 2:11 AM, Ralph Roberts via AMBER <amber.ambermd.org> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> Greetings to the Community.
> I am new to MD simulations and am trying to model a protein comprising the Fe2S2 cluster having four cysteine ligands. Can someone suggest what the error might be in executing MCPB.py?
>
> Here are my input files and the error message.
>
>
> Fe2S2 cluster with 4cystine residues (4x CYM; residues 125, 128, 586, 589).
>
>
> FE1.mol2
>
>
> .<TRIPOS>MOLECULE
>
> FES
>
> 1 0 1 0 0
>
> SMALL
>
> User Assigned Charge
>
>
>
>
>
> .<TRIPOS>ATOM
>
> 1 FE1 15.3160 -2.3050 29.6670 FE1 800 FES 3.000000
>
> .<TRIPOS>BOND
>
> .<TRIPOS>SUBSTRUCTURE
>
> 1 FES 1 TEMP 0 **** **** 0 ROOT
>
> ……………………………………………………………………………………………….
>
> FE2.mol2
>
>
> .<TRIPOS>MOLECULE
>
> FES
>
> 1 0 1 0 0
>
> SMALL
>
> User Assigned Charge
>
>
>
>
>
> .<TRIPOS>ATOM
>
> 1 FE2 17.7780 -3.7910 29.6470 FE2 800 FES 3.000000
>
> .<TRIPOS>BOND
>
> .<TRIPOS>SUBSTRUCTURE
>
> 1 FES 1 TEMP 0 **** **** 0 ROOT
>
> .
>
> ……………………………………………………………………………………………….
>
> S1.mol2
>
>
> .<TRIPOS>MOLECULE
>
> FES
>
> 1 0 1 0 0
>
> SMALL
>
> User Assigned Charge
>
>
>
>
>
> .<TRIPOS>ATOM
>
> 1 S1 17.4690 -1.4890 29.5430 S1 FES -2.000000
>
> .<TRIPOS>BOND
>
> .<TRIPOS>SUBSTRUCTURE
>
> 1 FES 1 TEMP 0 **** **** 0 ROOT
>
>
> ………………………………………………………………………………………….
>
> S2.mol2
>
>
> .<TRIPOS>MOLECULE
>
> FES
>
> 1 0 1 0 0
>
> SMALL
>
> User Assigned Charge
>
>
>
>
>
> .<TRIPOS>ATOM
>
> 2 S2 15.5720 -4.5270 29.7440 S2 800 FES -2.000000
>
> .<TRIPOS>BOND
>
> .<TRIPOS>SUBSTRUCTURE
>
> 1 FES 1 TEMP 0 **** **** 0 ROOT
>
>
> ………………………………………………………………………………………
>
> 1OHW_FIXED_H.pdb (Here I show the bottom of the file)
>
>
> ATOM 14607 OXT PHE 922 29.360 -6.511 71.257 1.00 0.00 O
>
> TER 14607 PHE 922
>
> HETATM14608 S1 FES A 923 17.469 -1.489 29.543 1.00 21.77 S
>
> HETATM14609 S2 FES A 923 15.572 -4.527 29.744 1.00 23.01 S
>
> HETATM14610 FE1 FES A 923 15.316 -2.305 29.667 1.00 18.83 FE
>
> HETATM14611 FE2 FES A 923 17.778 -3.791 29.647 1.00 21.66 FE
>
> END
>
>
> …………………………………………………………………………………………….
>
> 1OHW.in
>
>
> original_pdb 1OHW_FIXED_H.pdb
>
> group_name 1OHW
>
> cut_off 2.8
>
> ion_ids 14610 14611
>
> ion_mol2files FE1.mol2 FE2.mol2
>
> naa_mol2files S1.mol2 S2.mol2 <— Is this correct for the Fe2S2 complex???
>
> large_opt 1
>
>
> ………………………………………………………………………………….
>
>
> ******************************************************************
>
> The input file you are using is : 1OHW.in
>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>
> The following is the input variable you have:
>
> The variable ion_ids is : [14610, 14611]
>
> The variable ion_info is : []
>
> The variable ion_mol2files is : ['FE1.mol2', 'FE2.mol2']
>
> The variable original_pdb is : 1OHW_FIXED_H.pdb
>
> The variable add_bonded_pairs is : []
>
> The variable add_redcrd is : 0
>
> The variable additional_resids is : []
>
> The variable anglefc_avg is : 0
>
> The variable bondfc_avg is : 0
>
> The variable chgfix_resids is : []
>
> The variable cut_off is : 2.8
>
> The variable force_field is : ff19SB
>
> The variable frcmod_files is : []
>
> The variable gaff is : 1
>
> The variable group_name is : 1OHW
>
> The variable ion_paraset is : 12_6 (Only for the ions using the nonbonded model).
>
> The variable large_opt is : 1
>
> The variable lgmodel_chg is : -99
>
> The variable lgmodel_spin is : -99
>
> -99 means program will assign a charge automatically.
>
> The variable naa_mol2files is : ['S1.mol2', 'S2.mol2']
>
> The variable scale_factor is : 1.0
>
> ATTENTION: This is the scale factor of frequency. The
>
> force constants will be scaled by multiplying the square
>
> of scale_factor.
>
> The variable smmodel_chg is : -99
>
> The variable smmodel_spin is : -99
>
> -99 means program will assign a charge automatically.
>
> The variable software_version is : gau
>
> The variable sqm_opt is : 0
>
> The variable water_model is : OPC
>
> The variable xstru is : 0
>
> ******************************************************************
>
> * *
>
> *=======================Metal Site Information===================*
>
> * *
>
> ******************************************************************
>
> ***Selected Metal ion FE1 is atom 14610 in residue 923-FES
>
> ***Selected Metal ion FE2 is atom 14611 in residue 923-FES
>
> 125-CYM.SG is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
>
> 128-CYM.SG is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
>
> 923-FES.S1 is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
>
> 923-FES.S2 is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
>
> 586-CYM.SG is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
>
> 589-CYM.SG is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
>
> ***The following residues are in the Metal Site:
>
> Residue 125-CYM
>
> Residue 128-CYM
>
> Residue 586-CYM
>
> Residue 589-CYM
>
> Residue 923-FES
>
> ***The small model contains the following residues:
>
> [125, 128, 586, 589, 923]
>
> ***The large model contains the following residues:
>
> [124, 125, 126, 127, 128, 129, 585, 586, 587, 588, 589, 590, 923]
>
> ******************************************************************
>
> * *
>
> *=======================Building models==========================*
>
> * *
>
> ******************************************************************
>
> ***Creating the small model...
>
> It contains the residue 125-CYM as sidechain coordinated.
>
> It contains the residue 128-CYM as sidechain coordinated.
>
> It contains the residue 586-CYM as sidechain coordinated.
>
> It contains the residue 589-CYM as sidechain coordinated.
>
> It contains the residue 923-FES as normal.
>
> Totally there are 36 atoms in the small model.
>
> Totally there are 188 electrons in the small model.
>
> ***Creating the standard model...
>
> It contains the residue 125-CYM as normal.
>
> It contains the residue 128-CYM as normal.
>
> It contains the residue 586-CYM as normal.
>
> It contains the residue 589-CYM as normal.
>
> It contains the residue 923-FES as normal.
>
> Totally there are 44 atoms in the standard model.
>
> ***Creating the large model...
>
> Creating the residue 124-ALA into ACE...
>
> It contains the residue 125-CYM as normal.
>
> Creating the residue 126-GLY into GLY...
>
> Creating the residue 127-SER into GLY...
>
> It contains the residue 128-CYM as normal.
>
> Creating the residue 129-SER into NME...
>
> Creating the residue 585-ALA into ACE...
>
> It contains the residue 586-CYM as normal.
>
> Creating the residue 587-GLY into GLY...
>
> Creating the residue 588-SER into GLY...
>
> It contains the residue 589-CYM as normal.
>
> Creating the residue 590-SER into NME...
>
> It contains the residue 923-FES as normal.
>
> Totally there are 96 atoms in the large model.
>
> Totally there are 468 electrons in the large model.
>
> Traceback (most recent call last):
>
> File "/Users/ralph/anaconda3/bin/MCPB.py", line 651, in <module>
>
> gene_model_files(orpdbf, ionids, addres, addbpairs, gname, ff_choice,
>
> File "/Users/ralph/anaconda3/lib/python3.11/site-packages/pymsmt/mcpb/gene_model_files.py", line 1909, in gene_model_files
>
> build_large_model(mol, reslist, lmsresids, lmsresace, lmsresnme, lmsresgly,
>
> File "/Users/ralph/anaconda3/lib/python3.11/site-packages/pymsmt/mcpb/gene_model_files.py", line 1603, in build_large_model
>
> write_gau_mkf(outf, gmkf, lgchg, SpinNum, gatms, ionnames,
>
> File "/Users/ralph/anaconda3/lib/python3.11/site-packages/pymsmt/mol/gauio.py", line 286, in write_gau_mkf
>
> chg = int(round(chargedict[ionname], 0))
>
> ~~~~~~~~~~^^^^^^^^^
>
> KeyError: 'FE2'
>
>
> Regards,
>
> Ralph R. Roberts, PhD
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Received on Sat Dec 23 2023 - 01:00:03 PST
