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@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@H1 (etc.)




--

======================================================================

Dr Thomas Evangelidis

Research Scientist

IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences

Prague, Czech Republic
  & 
CEITEC - Central European Institute of Technology
Brno, Czech Republic 

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