ISOLDE: Unparameterised residue detected

[jimahjr@…]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/jimahjr/Desktop/MD/2020/model_building_consensus/5w7b_lps.pdb

> open
> /Users/jimahjr/Desktop/MD/2020/model_building_consensus/cryosparc_P6_J861__localfilter.mrc

Opened cryosparc_P6_J861__localfilter.mrc, grid size 240,240,240, pixel 1.07,
shown at level 0.203, step 1, values float32  

> clipper associate #2 toModel #1

> isolde start

> set selectionWidth 4

/Users/jimahjr/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/molobject.py:1978: RuntimeWarning: divide by zero
encountered in double_scalars  
self.global_k = scaling_constant/ref_g  
Done loading forcefield  

> addh

Summary of feedback from adding hydrogens to 5w7b_lps.pdb #1.2  
---  
notes | Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
1 hydrogens added  
  

> hide HC

> isolde restrain ligands #1

> select #1

220 atoms, 221 bonds, 8 residues, 14 models selected  

> isolde sim start sel

Loading residue template for FTT from internal database  
Loading residue template for MYR from internal database  
Loading residue template for PO4 from internal database  
Traceback (most recent call last):  
File "/Users/jimahjr/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2727, in start_sim  
self.params, self.sim_params, excluded_residues = self.ignored_residues)  
File "/Users/jimahjr/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 616, in __init__  
raise e  
File "/Users/jimahjr/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 595, in __init__  
isolde.forcefield_mgr)  
File "/Users/jimahjr/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1348, in __init__  
sim_params, residue_templates)  
File "/Users/jimahjr/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1430, in
_create_openmm_system  
raise RuntimeError('Unparameterised residue detected')  
RuntimeError: Unparameterised residue detected  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/Users/jimahjr/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/cmd.py", line 88, in isolde_sim  
isolde.start_sim()  
File "/Users/jimahjr/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2740, in start_sim  
self._unparam_mgr._sim_unparam_res_cb()  
File "/Users/jimahjr/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 207, in
_sim_unparam_res_cb  
self._show_main_frame()  
File "/Users/jimahjr/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 48, in
_show_main_frame  
self._update_unparameterised_residues_list()  
File "/Users/jimahjr/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/validation/unparameterised.py", line 87, in
_update_unparameterised_residues_list  
by_name, by_comp = ff.find_possible_templates(r)  
File "/Users/jimahjr/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/forcefields.py", line 339, in
find_possible_templates  
template = self._templates[tmpl_name]  
KeyError: 'GLYCAM_VYNP'  
  
KeyError: 'GLYCAM_VYNP'  
  
File "/Users/jimahjr/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/forcefields.py", line 339, in
find_possible_templates  
template = self._templates[tmpl_name]  
  
See log for complete Python traceback.  
  




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[Tristan Croll]

... huh. I'm at a bit of a loss to explain what could have caused that KeyError. Any chance I could take a look at the model (send off-list to tic20@… if you like)?

Also, there's an earlier warning in the log (divide by zero encountered) that suggests your model wasn't docked in the map prior to running "clipper associate"... you really need to have the model rigid-body docked first (and I clearly need to make sure that this is properly caught early, since it'll lead to weird and confusing problems later).

[john.jimah@…]

Hi Tristan,

Thank you. I’m trying to get MD parameters for a ligand… and even though I have phenix on my computer, the phenix plug in for Chimera doesn’t install properly. And I also get an error that phenix needs to be in an executable path.

Anyway, my main goal is to get MD parameters for the attached ligand. If you are able to provide me with those, my work will be much easier. Thank you!

-John



From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Thursday, April 22, 2021 at 1:45 PM
To:
Cc: Jimah, John (NIH/NIDDK) [F] <john.jimah@nih.gov>, tic20@cam.ac.uk <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4548: ISOLDE: Unparameterised residue detected
#4548: ISOLDE: Unparameterised residue detected
----------------------------------+---------------------------
          Reporter:  jimahjr@…    |      Owner:  Tristan Croll
              Type:  defect       |     Status:  assigned
          Priority:  normal       |  Milestone:
         Component:  Third Party  |    Version:
        Resolution:               |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+---------------------------

Comment (by Tristan Croll):

 ... huh. I'm at a bit of a loss to explain what could have caused that
 KeyError. Any chance I could take a look at the model (send off-list to
 tic20@cam.ac.uk if you like)?

 Also, there's an earlier warning in the log (divide by zero encountered)
 that suggests your model wasn't docked in the map prior to running
 "clipper associate"... you really need to have the model rigid-body docked
 first (and I clearly need to make sure that this is properly caught early,
 since it'll lead to weird and confusing problems later).

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4548#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

Jimah_lig1.pdb​

Jimah_ligand2.pdb​

[john.jimah@…]

Added by email2trac

[john.jimah@…]

Added by email2trac

[Tristan Croll]

Ah - that one's going to be a bit of a challenge, I'm afraid. ISOLDE doesn't currently support novel ligands with covalent bonds between each other or to protein/nucleic acid (getting that right is going to take a big effort). The files you've attached contain three ligands that are all covalently bonded to each other - your best bet for these would be to merge them together into a bigger "frankenligand" for ISOLDE's purposes, then split back out into three separate ligands later. Sorry about that - I'd love to have this part of things better developed, but the past year has slowed many things down.

More generally, to prepare a standalone ligand for ISOLDE, it's currently easiest to do the first step from the command line:

phenix.elbow --amber {your ligand file}

Then start ChimeraX and ISOLDE in that directory, and do:

ISOLDE/Prep/Convert Amber Files

... and you should now have a file called {ligand id}.xml in your working directory that you can load with ISOLDE's "Load residue MD definition(s)" button.


It turns out that what caused the actual traceback is a separate issue. I take it you have a D-glucosamine residue (PA1) in your model... a somewhat rare occurrence that it appears hasn't come up for ISOLDE yet. Looks like there's something wrong with how I have ISOLDE trying to assign it to a template in the GLYCAM forcefield (which is a bit of a temperamental beast... will look into it).
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 22 April 2021 19:04
Cc: jimahjr@nih.gov <jimahjr@nih.gov>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4548: ISOLDE: Unparameterised residue detected

#4548: ISOLDE: Unparameterised residue detected
----------------------------------+---------------------------
          Reporter:  jimahjr@…    |      Owner:  Tristan Croll
              Type:  defect       |     Status:  assigned
          Priority:  normal       |  Milestone:
         Component:  Third Party  |    Version:
        Resolution:               |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+---------------------------
Changes (by john.jimah@…):

 * Attachment "Jimah_ligand2.pdb" added.

 Added by email2trac

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4548>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker