Hi Barak,
The atom names in your PDB file and mol2 file do not match with each other. There should be a one-to-one match for these atom names in the PDB and mol2 files.
In the GD-MD2.pdb file, inside the UNL residue, you have multiple atoms share the same atom name, while in your UNL.mol2 file each atoms have different atom names.
You need to have your PDB file with each atom inside a certain residue has a different atom name, and these atom names should correctly match the atom names inside the corresponding mol2 file(s), in order to prevent MCPB.py falsely recognizing them.
Hope it helps,
Pengfei
> On Jun 8, 2020, at 7:19 AM, Barak Alnami <barak.alnami.postgrad.manchester.ac.uk> wrote:
>
>
>
>
> Hi folks ,
>
> I need some help with MCPB.py am trying to get a force field parameter for my molecule. without the the protein chain. please find the attached files that I needed to complete the first step (Generate the PDB, Gaussian, GAMESS-US and fingerprint modeling files). However, I get this type or error :
>
>
> *=======================Metal Site Information===================*
>
> * *
>
> ******************************************************************
>
> ***Selected Metal ion GD is atom 1 in residue 1-GD
>
> 2-UNL.O is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
>
> 2-UNL.OXT is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
>
> 2-UNL.OXT is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
>
> 2-UNL.N is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
>
> 2-UNL.N is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
>
> 2-UNL.N is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
>
> 2-UNL.N is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
>
> 2-UNL.N is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
>
> 2-UNL.N 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 1-GD
>
> Residue 2-UNL
>
> Traceback (most recent call last):
>
> File "/Users/abubarak/anaconda3/bin/MCPB.py", line 644, in <module>
>
> addred, lgchg, lgspin)
>
> File "/Users/abubarak/anaconda3/lib/python3.6/site-packages/pymsmt/mcpb/gene_model_files.py", line 1690, in gene_model_files
>
> totchg = totchg + chargedict['C' + mol.residues[i].resname]
>
> KeyError: 'CUNL'
>
> It would be great if someone can help me with this.
>
> Thanks
> Barak
> <GD-MD.pdb><GD-MD2.pdb><GD.mol2><GD.pdb><GdL-MD.in><GdL-MD.pdb><UNL.frcmod><UNL.mol2><UNL.pdb>_______________________________________________
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Received on Thu Jun 11 2020 - 09:00:03 PDT
