[Chimera-users] create automatically all alternative protonation states of protein

[Eric Pettersen]

Hi Thomas,
	Addcharge is what adds GAFF types.  What exact addcharge command or function call are you using?

—Eric

> On Apr 1, 2019, at 2:25 PM, Thomas Evangelidis <tevang3 at gmail.com> wrote:
> 
> Hi Eric,
> 
> Thanks, but it seems that it doesn't recognize one of ligand's hydrogens, which is strange because I calculate AM1 charges before adding ions. This is the whole error message. I also attach the input files. Do you have any idea about what might be wrong?
> 
> Traceback (most recent call last):
>   File "/home/thomas/Programs/Anaconda2/envs/ete3/bin/pychimera", line 12, in <module>
>     update_dict = pychimera.__main__.run()
>   File "/home/thomas/Programs/Anaconda2/envs/ete3/lib/python2.7/site-packages/pychimera/__main__.py", line 6, in run
>     pychimera.main()
>   File "/home/thomas/Programs/Anaconda2/envs/ete3/lib/python2.7/site-packages/pychimera/core.py", line 347, in main
>     run_cli_options(args)
>   File "/home/thomas/Programs/Anaconda2/envs/ete3/lib/python2.7/site-packages/pychimera/core.py", line 309, in run_cli_options
>     globals().update(runpy.run_path(choice, run_name="__main__"))
>   File "/home/thomas/Programs/Anaconda2/envs/ete3/lib/python2.7/runpy.py", line 252, in run_path
>     return _run_module_code(code, init_globals, run_name, path_name)
>   File "/home/thomas/Programs/Anaconda2/envs/ete3/lib/python2.7/runpy.py", line 82, in _run_module_code
>     mod_name, mod_fname, mod_loader, pkg_name)
>   File "/home/thomas/Programs/Anaconda2/envs/ete3/lib/python2.7/runpy.py", line 72, in _run_code
>     exec code in run_globals
>   File "/usr/local/bin/protonate_receptor.py", line 300, in <module>
>     write_protonated_structure(protonations)
>   File "/usr/local/bin/protonate_receptor.py", line 129, in write_protonated_structure
>     initiateAddions(models, "Cl-", "neutralize", chimera.replyobj.status)
>   File "/home/thomas/Programs/Chimera/share/Addions/__init__.py", line 72, in initiateAddions
>     noGaffComplain(noGaff, "Add Ions")
>   File "/home/thomas/Programs/Chimera/share/WritePrmtop/__init__.py", line 10, in noGaffComplain
>     raise ValueError("Cannot determine GAFF type for %s (etc.)" % noGaff[0])
> ValueError: Cannot determine GAFF type for #1:1 at H1 (etc.)
> 
> 
> 
> 
> -- 
> ======================================================================
> Dr Thomas Evangelidis
> Research Scientist
> IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>
> Prague, Czech Republic
>   & 
> CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>
> Brno, Czech Republic 
> 
> email: tevang3 at gmail.com <mailto:tevang3 at gmail.com>
> website: https://sites.google.com/site/thomasevangelidishomepage/ <https://sites.google.com/site/thomasevangelidishomepage/>
> 
> 
> <1a30_protein.pdb><1a30_ligand.sdf>_______________________________________________
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