Thanks Dr.Preeti for the suggestion. That fixed the problem.
Regards
Gagandeep Singh
On Sat, 1 Aug, 2020, 2:50 am Preeti Pandey, <preetipandey2806.gmail.com>
wrote:
> 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:
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > **=======================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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
>
>
>
> *Regards *
>
>
> *PREETI PANDEY (Ph. D.)*
>
> -
>
>
> -
>
>
> -
>
>
> -
>
> *Postdoctoral Research Associate*
> *Department of Chemistry & Biochemistry*
> *University of Oklahoma*
>
> *101 Stephenson ParkwayNorman, OK 73019-5251, USA*
> _______________________________________________
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>
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Received on Sat Aug 01 2020 - 19:00:03 PDT
