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

[Thomas Evangelidis]

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

website: https://sites.google.com/site/thomasevangelidishomepage/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20190401/6bbbe79c/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 1a30_protein.pdb
Type: chemical/x-pdb
Size: 144607 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20190401/6bbbe79c/attachment.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 1a30_ligand.sdf
Type: application/octet-stream
Size: 3395 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20190401/6bbbe79c/attachment.obj>