[Chimera-users] Chimera help - attempted to do minimization
Jia Hao Chen
jche486 at uwo.ca
Thu Jul 2 09:12:03 PDT 2020
Thanks so much for your help.
From: Eric Pettersen <pett at cgl.ucsf.edu>
Sent: Thursday, July 2, 2020 12:09 PM
To: Jia Hao Chen <jche486 at uwo.ca>
Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Chimera help - attempted to do minimization
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.
UCSF Computer Graphics Lab
On Jul 1, 2020, at 8:17 PM, Jia Hao Chen <jche486 at uwo.ca<mailto:jche486 at uwo.ca>> wrote:
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
I've attached the reply log for more details. Please let me know if I need to fix anything, thank you.
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