Gentle reminder!
On Sat, 25 Jul, 2020, 3:25 am gagandeep singh, <gagan.sk.1994.gmail.com>
wrote:
> Hi All,
> I was running MCPB.py fto prepare gaussian file for my system having Fe2+
> ion surrounded by ASp and AKG. It gave the following error:
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> **=======================Building models==========================**
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> **********************************************************************Creating
> the small model...It contains the residue 126-ASP as sidechain
> coordinated.It contains the residue 206-FE as normal.It contains the
> residue 207-AKG as normal.Totally there are 27 atoms in the small
> model.Totally there are 137 electrons in the small model.***Creating the
> standard model...It contains the residue 126-ASP as normal.Traceback (most
> recent call last): File "/home/gsk/miniconda3/bin/MCPB.py", line 644, in
> <module> addred, lgchg, lgspin) File
> "/home/gsk/miniconda3/lib/python3.7/site-packages/pymsmt/mcpb/gene_model_files.py",
> line 1908, in gene_model_files bdedatms, addbpairs, libdict, autoattyp)
> File
> "/home/gsk/miniconda3/lib/python3.7/site-packages/pymsmt/mcpb/gene_model_files.py",
> line 1472, in build_standard_model attype = libdict[resname + '-' +
> atname][0]KeyError: 'ASP-HB1'*
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> Looks like there is a problem with my pdb file and naming of residues is
> not compatible with amber. I saved the pdb in chimera with the output
> option for serial numbering as amber,still got this error.
> Any suggestions on how to prepare my protein in order to overcome this
> error?
> Thanks.
> Regards
> Gagandeep Singh
>
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Received on Fri Jul 31 2020 - 14:30:02 PDT
