Dear MCPB delveloper,
I am sorry for my late reply. The solfware I used to add H is pymol. Thank
you so much for your help.
Best regards,
Chính
On Tue, Sep 5, 2017 at 7:33 PM, Pengfei Li <ambermailpengfei.gmail.com>
wrote:
> Hi Chinh,
>
> This is because the names of H atoms in your PDB file doesn’t follow the
> PDB version 3.0 style. Which software did you use to add hydrogens? I
> suggest you to use the H++ web server: http://biophysics.cs.vt.edu/ <
> http://biophysics.cs.vt.edu/>.
>
> Kind regards,
> Pengfei
>
> > On Sep 4, 2017, at 6:09 AM, Lê Ngọc Chính <lengocchinh2306.gmail.com>
> wrote:
> >
> > Dear
> > I have met this error when using MCPB.py
> > ******************************************************************
> > * *
> > *=======================Building models==========================*
> > * *
> > ******************************************************************
> > ***Creating the small model...
> > It contains the residue 90-HID as sidechain coordinated.
> > It contains the residue 221-GLN as sidechain coordinated.
> > It contains the residue 223-TYR as sidechain coordinated.
> > It contains the residue 233-CU as keeping sidechain and CO group.
> > It contains the residue 234-HIC as keeping sidechain and NH group.
> > Totally there are 70 atoms in the small model.
> > Totally there are 259 electrons in the small model.
> > ***Creating the standard model...
> > It contains the residue 90-HID as normal.
> > Traceback (most recent call last):
> > File "/home/admin/Duc/amber16/bin/MCPB.py", line 562, in <module>
> > premol2fs, cutoff, watermodel, 2, largeopt, sqmopt, smchg, lgchg)
> > File
> > "/home/admin/Duc/amber16/lib/python2.7/site-packages/mcpb/
> gene_model_files.py",
> > line 1742, in gene_model_files
> > bdedatms, libdict, autoattyp)
> > File
> > "/home/admin/Duc/amber16/lib/python2.7/site-packages/mcpb/
> gene_model_files.py",
> > line 1319, in build_standard_model
> > attype = libdict[resname + '-' + atname][0]
> > KeyError: 'HID-H01'
> >
> > Can you help me to solve it? Thanks so much.
> > --
> > Chính
> > <HIC.frcmod><CU.mol2><4opb.pdb><HIC.mol2><4opb_fix1.pdb><
> CU.in>_______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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--
Chính
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Received on Sun Sep 10 2017 - 09:30:02 PDT
