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

[Thomas Evangelidis]

import chimera
from Addions import initiateAddions
from DockPrep import prep

models = chimera.openModels.list(modelTypes=[chimera.Molecule])
print "Preparing receptor for docking and calculating ligand AM1
charges (may be slow)."
prep(models, nogui=True, method='am1')

# and after I change the protonations

rc("addcharge std spec #0") # re-add ff14SB charges to the protonated
receptor only (the ligand protonation did not change)

initiateAddions(models, "Cl-", "neutralize", chimera.replyobj.status)



On Tue, 2 Apr 2019 at 00:23, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> 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
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
>
>
> <1a30_protein.pdb><1a30_ligand.sdf>
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>
>

-- 

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

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/
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