ISOLDE and reporting error

[DLMLEN001@…]

Good day,

I am trying to run a simulation on ISOLDE and I get a error
''Exception: Multiple matching templates found for residue 344 (HOH): OHE, GLYCAM_ROH.

File "C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\app\forcefield.py", line 893, in _getResidueTemplateMatches
raise Exception('Multiple matching templates found for residue %d (%s): %s.' % (res.index+1, res.name, ', '.join(match[0].name for match in allMatches)))''

A new window opens prompting me to report the bug but I get an error message that there was an error submitting and I should send an email to this address.

Please note that there is no residue 344 or a water with that number in my model and I am able to run simulations when the map is a .mrc file, but I get this error with .mtz files.


Lenye Dlamini
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[Tristan Croll]

Hi Lenye,

Sorry about the unedifying error message (it's a traceback from the underlying OpenMM library, and the number reported is the index of the offending residue in the simulation rather than its RESID). The cause is that a water is missing a hydrogen, and OpenMM doesn't know what to do with it. The most common cause of this is that you have a water in a tightly constrained environment near a metal, causing AddH to skip adding the second hydrogen. Try running addh metaldist 1 to see if that helps. If it still fails, try copy/pasting the following script into the shell (Tools/General/Shell):

m = session.isolde.selected_model
waters = m.residues[m.residues.names=='HOH']
for w in waters:
    if len(w.atoms) != 3:
        print('{}{} has the wrong number of atoms'.format(w.chain_id, w.number))

That'll pinpoint the offender(s) for you. To delete a water, use del #{model}/{chain}/{number} in the command line (you can also select the residue and then do del sel - but I'd caution against that to avoid accidentally deleting something you don't want to lose).

}}}

[Tristan Croll]

The new ISOLDE builds (once released) will give more helpful error messages for cases like this.

[DLMLEN001@…]

Hello,

Thank you.
Problem fixed.

Lenye
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, May 25, 2020 5:57 PM
Cc: Lenye Dlamini <DLMLEN001@myuct.ac.za>; tic20@cam.ac.uk <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #3300: ISOLDE and reporting error

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#3300: ISOLDE and reporting error
----------------------------------+---------------------------
          Reporter:  DLMLEN001@…  |      Owner:  Tristan Croll
              Type:  defect       |     Status:  closed
          Priority:  normal       |  Milestone:
         Component:  Third Party  |    Version:
        Resolution:  fixed        |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+---------------------------
Changes (by Tristan Croll):

 * status:  assigned => closed
 * resolution:   => fixed


Comment:

 The new ISOLDE builds (once released) will give more helpful error
 messages for cases like this.

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