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@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@cgl.ucsf.edu <mailto:pett@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@gmail.com <mailto: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 <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@gmail.com <mailto:tevang3@gmail.com> website: https://sites.google.com/site/thomasevangelidishomepage/ <https://sites.google.com/site/thomasevangelidishomepage/>
<1a30_protein.pdb><1a30_ligand.sdf>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <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@gmail.com <mailto:tevang3@gmail.com> website: https://sites.google.com/site/thomasevangelidishomepage/ <https://sites.google.com/site/thomasevangelidishomepage/>
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