Hi Abhilash,
This is because there is no one to one match inside the comp_H_renum.pdb and COB.mol2 files.
Change the atom number 182 to have reside ID as 2 and residue name as “CO" in the comp_H_renum.pdb file, the problem would be solved.
Kind regards,
Pengfei
> On Mar 8, 2017, at 3:45 AM, Abhilash J <md.scfbio.gmail.com> wrote:
>
> Hi everyone,
>
> I am having trouble in parameterizing CO-METHYLCOBALAMIN (
> https://www3.rcsb.org/ligand/cob) with MCPB.py.
> I am able to generate comp_small_opt.com and comp_small_fc.com but
> standard model fails.
> I am attaching the files i used to generate the parameters and initial
> start files for your reference.
>
> ******************************************************************
> * *
> *=======================Building models==========================*
> * *
> ******************************************************************
> ***Creating the small model...
> It contains the residue 1-COB as normal.
> Totally there are 182 atoms in the small model.
> Totally there are 687 electrons in the small model.
> ***Creating the standard model...
> It contains the residue 1-COB as normal.
> Traceback (most recent call last):
> File "/home/abhilash/amber16/bin/MCPB.py", line 562, in <module>
> premol2fs, cutoff, watermodel, 2, largeopt, sqmopt, smchg, lgchg)
> File
> "/home/abhilash/amber16/lib/python2.7/site-packages/mcpb/gene_model_files.py",
> line 1742, in gene_model_files
> bdedatms, libdict, autoattyp)
> File
> "/home/abhilash/amber16/lib/python2.7/site-packages/mcpb/gene_model_files.py",
> line 1319, in build_standard_model
> attype = libdict[resname + '-' + atname][0]
> *KeyError: 'COB-CO*'
>
>
>
>
> Regards
>
> Abhilash
> <CO.mol2><COB.frcmod><COB.mol2><comp.in><comp_H_renum.pdb><CO.pdb><COB_2.pdb>_______________________________________________
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Received on Tue Mar 14 2017 - 14:30:03 PDT
