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

Fri Apr 5 04:08:18 PDT 2019

Hi Eric,

I think I found what is wrong. When I do prep() and then split and combine
models from the original, the new modes loss their atom types (?). Is this
correct? I was led to this conclusion because if I do another prep() to the
combined model then I do not get no-GAFF error during initiateAddions().

best,
Thomas

On Tue, 2 Apr 2019 at 01:15, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> If I do just the commands you provided below on the models you attached
> earlier 1a30_protein/ligand, I do not get the no-GAFF error you got.  I get
> a different (and later) error that is going to be problematic.  Add Ions
> does not work on multiple models in aggregate — if given multiple models it
> will add ions to each separately, which is an issue since you’ve separated
> your receptor and ligand into different models.  If you add ions to just
> the receptor, it could very well place one in the ligand binding pocket.
> If you combine your ligand and receptor into a single model, that could
> work but would be more complicated and will probably be a headache. :-(
>
> Anyway, I’ve attached the script I used that did not get the GAFF error so
> you can try it yourself on the 1a30 system.  You could let me know what
> additional factors are needed to get the no-GAFF error, assuming that the
> other Add Ions issue isn’t a showstopper.
>
> —Eric
>
>
>
> On Apr 1, 2019, at 3:33 PM, Thomas Evangelidis <tevang3 at gmail.com> wrote:
>
> 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/
>
>
>
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription:
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
>

-- 

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

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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