Please fix the names of the hydrogens bonded to the C-beta carbon of
aspartic acid to HB2 and HB3.
On Fri, Jul 31, 2020 at 4:01 PM gagandeep singh <gagan.sk.1994.gmail.com>
wrote:
> 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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> >
> >
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> >
> >
> > **=======================Building models==========================**
> >
> >
> **********************************************************************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'*
> >
> > 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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--
*Regards *
*PREETI PANDEY (Ph. D.)*
-
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-
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*Postdoctoral Research Associate*
*Department of Chemistry & Biochemistry*
*University of Oklahoma*
*101 Stephenson ParkwayNorman, OK 73019-5251, USA*
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Received on Fri Jul 31 2020 - 14:30:04 PDT
