[AMBER] MCPB.py problem to make step 1 works from Barak Alnami on 2020-06-08 (Amber Archive Jun 2020)

From: Barak Alnami <barak.alnami.postgrad.manchester.ac.uk>
Date: Mon, 8 Jun 2020 11:19:56 +0000

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

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chemical/x-pdb attachment: GD-MD.pdb

chemical/x-pdb attachment: GD-MD2.pdb

chemical/x-mol2 attachment: GD.mol2

chemical/x-pdb attachment: GD.pdb

application/octet-stream attachment: GdL-MD.in

chemical/x-pdb attachment: GdL-MD.pdb

application/octet-stream attachment: UNL.frcmod

chemical/x-mol2 attachment: UNL.mol2

chemical/x-pdb attachment: UNL.pdb

Received on Mon Jun 08 2020 - 04:30:02 PDT