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

Fri Apr 5 12:47:26 PDT 2019

You are correct.  The idatmType attribute of atoms was not copied.  Explicitly setting idatmTypes isn’t something that happens a lot, so it got overlooked in the copy/combine code.  I have fixed that oversight.  In tomorrow’s build, idatmTypes that were explicitly set will be copied.

—Eric

> On Apr 5, 2019, at 4:08 AM, Thomas Evangelidis <tevang3 at gmail.com> wrote:
> 
> 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 <mailto: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 <mailto: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 <mailto: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 <mailto: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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>> 
>> 
>> 
>> -- 
>> ======================================================================
>> 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/>
>> 
>> 
>> _______________________________________________
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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 <mailto:tevang3 at gmail.com>
> website: https://sites.google.com/site/thomasevangelidishomepage/ <https://sites.google.com/site/thomasevangelidishomepage/>
> 
> 

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