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> 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> 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
website: https://sites.google.com/site/thomasevangelidishomepage/
<1a30_protein.pdb><1a30_ligand.sdf> _______________________________________________ Chimera-users mailing list: Chimera-users@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@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/