Hi Pengfei,
It worked, thanks for the help.
Regards
Abhilash
On Wed, Mar 15, 2017 at 2:49 AM, Pengfei Li <ambermailpengfei.gmail.com>
wrote:
> 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>_______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Wed Mar 15 2017 - 05:00:02 PDT
