Hi Jue,
I think there is something wrong with at least one atom name in your PDB file. That atom name has the first letter as “2” instead of an atomic symbol such as “N” or “H”.
Hope it helps,
Pengfei
> On Mar 4, 2020, at 10:41 PM, wujue <wuj18650693661.163.com> wrote:
>
> Distinguished Sir or Madam
>
> I'm trying to use MCPB.py for performing parameterizations for both the metalloprotein and organometallic compound systems. I followed the steps to prepare the PDB and mol2 files for the non-standard residues and metal ions in the tutorial and there was errors in the first step of generating the PDB, Gaussian and fingerprint modeling files.
>
> Here are my error messages:
>
> *****************************************************************
>
> * *
>
> *=======================Metal Site Information===================*
>
> * *
>
> ******************************************************************
>
> ***Selected Metal ion NI is atom 37834 in residue 2476-NI1
>
> 146-GLN.OE1 is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
>
> 2475-F31.NA is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
>
> 2475-F31.NB is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
>
> 2475-F31.NC is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
>
> 2475-F31.ND 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 146-GLN
>
> Residue 2475-F31
>
> Residue 2476-NI1
>
> ***The small model contains the following residues:
>
> [146, 2475, 2476]
>
> ***The large model contains the following residues:
>
> [145, 146, 147, 2475, 2476]
>
> ******************************************************************
>
> * *
>
> *=======================Building models==========================*
>
> * *
>
> ******************************************************************
>
> ***Creating the small model...
>
> It contains the residue 146-GLN as sidechain coordinated.
>
> It contains the residue 2475-F31 as normal.
>
> It contains the residue 2476-NI1 as normal.
>
> Totally there are 125 atoms in the small model.
>
> Traceback (most recent call last):
>
> File "/usr/local/theochem/amber16/amber16/bin/MCPB.py", line 644, in <module>
>
> addred, lgchg, lgspin)
>
> File "/usr/local/theochem/amber16/amber16/lib/python2.7/site-packages/pymsmt/mcpb/gene_model_files.py", line 1895, in gene_model_files
>
> smspin, addred, outf, sqmopt)
>
> File "/usr/local/theochem/amber16/amber16/lib/python2.7/site-packages/pymsmt/mcpb/gene_model_files.py", line 1380, in build_small_model
>
> AtNum = Atnum[gatm.element]
>
> KeyError: '2'
>
> This problem confused me. I tried to rebuild the model and repeat the preparations in the tutorials. It seems to be that the number of electrons in the model is wrong. But I don't know how to solve it.
>
> Could someone help me out of the problem? Any response will be highly appreciated!
> Yours,
> Wu Jue
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 27 2020 - 14:30:01 PDT
