Chimera help - attempted to do minimization
Hello, I attempted to do minimization on my mutant protein but I get this error when I try to run it: AttributeError: '_molecule.Atom' object has no attribute 'gaffType' File "C:\Program Files\Chimera 1.14\share\MMMD\MMTKinter.py", line 695, in _addStandardResidue "amber_atom_type": a.gaffType, I've attached the reply log for more details. Please let me know if I need to fix anything, thank you. Best regards, Jay Chen
Hi Jay, When Chimera assigns partial charges and atom types to standard residues, it simply looks up the name of the atom in a table. That means that the atoms in standard residues need to have their PDB standard names. The standard names for the hydrogens attached to CD1 in ILE residues are HD11, HD12, and HD13. In your structure those names are HD1, HD2, and HD3. You need to correct your structure so that those atoms have their standard names. One way is for you to edit your file. Another way is to delete all the hydrogens in Chimera and let Chimera add them back, which will result in them having the standard names. You do that by opening he command line (Favorites→Command Line) and typing the command "del H". After that, your minimization should work. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Jul 1, 2020, at 8:17 PM, Jia Hao Chen <jche486@uwo.ca> wrote:
Hello,
I attempted to do minimization on my mutant protein but I get this error when I try to run it: AttributeError: '_molecule.Atom' object has no attribute 'gaffType'
File "C:\Program Files\Chimera 1.14\share\MMMD\MMTKinter.py", line 695, in _addStandardResidue "amber_atom_type": a.gaffType, I've attached the reply log for more details. Please let me know if I need to fix anything, thank you.
Best regards,
Jay Chen <chimera_reply_log.txt>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
Hi Eric, Thanks so much for your help. Jay Chen ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Thursday, July 2, 2020 12:09 PM To: Jia Hao Chen <jche486@uwo.ca> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Chimera help - attempted to do minimization Hi Jay, When Chimera assigns partial charges and atom types to standard residues, it simply looks up the name of the atom in a table. That means that the atoms in standard residues need to have their PDB standard names. The standard names for the hydrogens attached to CD1 in ILE residues are HD11, HD12, and HD13. In your structure those names are HD1, HD2, and HD3. You need to correct your structure so that those atoms have their standard names. One way is for you to edit your file. Another way is to delete all the hydrogens in Chimera and let Chimera add them back, which will result in them having the standard names. You do that by opening he command line (Favorites→Command Line) and typing the command "del H". After that, your minimization should work. --Eric Eric Pettersen UCSF Computer Graphics Lab On Jul 1, 2020, at 8:17 PM, Jia Hao Chen <jche486@uwo.ca<mailto:jche486@uwo.ca>> wrote: Hello, I attempted to do minimization on my mutant protein but I get this error when I try to run it: AttributeError: '_molecule.Atom' object has no attribute 'gaffType' File "C:\Program Files\Chimera 1.14\share\MMMD\MMTKinter.py", line 695, in _addStandardResidue "amber_atom_type": a.gaffType, I've attached the reply log for more details. Please let me know if I need to fix anything, thank you. Best regards, Jay Chen <chimera_reply_log.txt>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Eric Pettersen -
Jia Hao Chen