Hi Fulbabu,
This is because the RU ion was not treated as a independent residue in the PDB file.
Please read the information in the tutorial carefully, which will save you a lot of time during the parameterization:
For example, your error can be avoided if you took the following advice in the tutorial:
"MCPB.py now supports more than 80 metal ions (see Figure 3 in the reference paper <
http://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00674>). For all of these metal ions and halide ions (if in the ion format but not neutral format), capitalized element name are suggested to use for both the residue name and atom name. Please make sure the residue name and atom name of the metal ion (not only for iron used here) are all captilized (e.g. herein all equals "FE", not "Fe", "fE", or "fe"), only in this way MCPB.py will recognize it as a metal ion. Meanwhile, please make sure each metal ion or halide ion (if it is in its ion format but not neutral format) is treated seperately as an indepedent residue in the PDB file. If you have metal site which has metal ion embeded in the ligand residue, for example, the HEME group in PDB file, please seperate the metal ion into an independent residue (also, with an unique residue number and atom number)in the PDB file. Meanwhile, in order to make MCPB.py recognize the atoms well
, if you have atoms have atom names capitalized with numbers in your original PDB file (applies for protein or ligand), please change these atom names to atom names capitalized with their element symbols (for example, change "2HA1" to "HA12", change "1HAA" to "HAA1") in the PDB file before performing following steps."
Hope it helps,
Pengfei
> On Feb 6, 2019, at 4:30 AM, Fulbabu Sk <phd1701171005.iiti.ac.in> wrote:
>
> Hi, Dr. Pengfei Li and Amber users,
> I am currently trying to create topology (prmtop) and coordinate (inpcrd)
> for a small molecule *OCTAHEDRAL RU-PYRIDOCARBAZOLE* (FLL) of PDB id*
> 3FXZ. *I followed the Amber tutorial
>
> *http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm
> <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm>*
> but Generate the PDB, Gaussian, GAMESS-US and fingerprint modeling files
> with the command line
>
>
> *MCPB.py -i FLL.in -s 1*
> there is a key error
>
> ***Creating the small model...
> It contains the residue 1-FLL as normal.
> Totally there are 62 atoms in the small model.
> Traceback (most recent call last):
> File "/home/fulbabu/program/amber16/bin/MCPB.py", line 644, in <module>
> addred, lgchg, lgspin)
> File
> "/home/fulbabu/program/amber16/lib/python2.7/site-packages/pymsmt/mcpb/gene_model_files.py",
> line 1895, in gene_model_files
> smspin, addred, outf, sqmopt)
> File
> "/home/fulbabu/program/amber16/lib/python2.7/site-packages/pymsmt/mcpb/gene_model_files.py",
> line 1380, in build_small_model
> AtNum = Atnum[gatm.element]
> KeyError: 'R'
>
> I couldn't understand how to fix it?
> My all files are attached below,
>
>
>
>
>
> ***************
> Kind regards
>
> *Md Fulbabu Sk*
>
>
>
> *Ph.D. Research ScholarDiscipline of BioSciences and Biomedical Engineering
> (BSBE)Indian Institute of Technology Indore (IITI), India*
> Computational BioPhysics Group IITI (Kar's Lab)
> <https://iitibsbeparimalkar.wixsite.com/biophysics>
> <RU.mol2><FLL.in><FLL.mol2><FLL_new_renum.pdb>_______________________________________________
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Received on Fri Feb 08 2019 - 19:00:02 PST
