Opened 7 weeks ago

Closed 6 weeks ago

#18851 closed defect (duplicate)

OpenMM compiler failure on Windows

Reported by: cwa5555@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.11.dev202509190047 (2025-09-19 00:47:43 UTC)
Description
repeat of previous with input file attached
trying to minimize this 10 residue peptide
thank you !
here is log :

openmm.OpenMMException: Error compiling kernel: :204:24: warning: double precision constant requires cl_khr_fp64, casting to single precision
const real PI = (real) 3.14159265358979323846;
^
fcl build 1 succeeded.
error: undefined reference to `_Z8atom_addPU3AS1mm()'

error: midlevel compiler failed build. 

File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-packages\openmm\openmm.py", line 5082, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
^^^^^^^^^^^^^^^^^^^^^^^^^^

See log for complete Python traceback.

Log:
UCSF ChimeraX version: 1.11.dev202509190047 (2025-09-19)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/jl80/Documents/10mer.pdb

Summary of feedback from opening C:/Users/jl80/Documents/10mer.pdb  
---  
warning | Ignored bad PDB record found on line 1  
REMARK 10mer  
  
Chain information for 10mer.pdb #1  
---  
Chain | Description  
A | No description available  
  

> minimize

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
Swapping /A GLY 10 to GLY  
Summary of feedback from adding hydrogens to 10mer.pdb #1  
---  
notes | No usable SEQRES records for 10mer.pdb (#1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: /A HIS 1  
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: /A GLY 10  
1 hydrogen bonds  
/A GLY 10 is not terminus, removing H atom from 'C'  
69 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 322, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 41, in cmd_minimize  
dock_prep_caller(session, [structure], memorize_name="minimization",
nogui=True,  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 146, in dock_prep_caller  
run_steps(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 107, in prep  
callback(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\addh\dock_prep.py", line 56, in run_for_dock_prep  
callback(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\add_charge\dock_prep.py", line 58, in run_for_dock_prep  
callback(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 156, in run_steps  
callback()  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 106, in <lambda>  
state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb())  
^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 43, in <lambda>  
steps=max_steps: _minimize(ses, struct, updates, log, steps), **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 171, in _minimize  
system = forcefield.createSystem(top, nonbondedCutoff=1*nanometer,
constraints=HBonds)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\openmm\app\forcefield.py", line 1280, in createSystem  
raise Exception(msg)  
Exception: Could not find typename 'N' for atom '<Atom 136 (N) of chain 0
residue 9 (A-GLY-10)>' in list of known atom types.  
Known atom types are: dict_keys(['tip3pfb_standard-Li+', 'tip3pfb_standard-
Na+', 'tip3pfb_standard-K+', 'tip3pfb_standard-Rb+', 'tip3pfb_standard-Cs+',
'tip3pfb_standard-F-', 'tip3pfb_standard-Cl-', 'tip3pfb_standard-Br-',
'tip3pfb_standard-I-', 'tip3pfb_standard-Be2+', 'tip3pfb_standard-Cu2+',
'tip3pfb_standard-Ni2+', 'tip3pfb_standard-Pt2+', 'tip3pfb_standard-Zn2+',
'tip3pfb_standard-Co2+', 'tip3pfb_standard-Pd2+', 'tip3pfb_standard-Ag2+',
'tip3pfb_standard-Cr2+', 'tip3pfb_standard-Fe2+', 'tip3pfb_standard-Mg2+',
'tip3pfb_standard-V2+', 'tip3pfb_standard-Mn2+', 'tip3pfb_standard-Hg2+',
'tip3pfb_standard-Cd2+', 'tip3pfb_standard-Yb2+', 'tip3pfb_standard-Ca2+',
'tip3pfb_standard-Sn2+', 'tip3pfb_standard-Pb2+', 'tip3pfb_standard-Eu2+',
'tip3pfb_standard-Sr2+', 'tip3pfb_standard-Sm2+', 'tip3pfb_standard-Ba2+',
'tip3pfb_standard-Ra2+', 'tip3pfb_standard-Al3+', 'tip3pfb_standard-Fe3+',
'tip3pfb_standard-Cr3+', 'tip3pfb_standard-In3+', 'tip3pfb_standard-Tl3+',
'tip3pfb_standard-Y3+', 'tip3pfb_standard-La3+', 'tip3pfb_standard-Ce3+',
'tip3pfb_standard-Pr3+', 'tip3pfb_standard-Nd3+', 'tip3pfb_standard-Sm3+',
'tip3pfb_standard-Eu3+', 'tip3pfb_standard-Gd3+', 'tip3pfb_standard-Tb3+',
'tip3pfb_standard-Dy3+', 'tip3pfb_standard-Er3+', 'tip3pfb_standard-Tm3+',
'tip3pfb_standard-Lu3+', 'tip3pfb_standard-Hf4+', 'tip3pfb_standard-Zr4+',
'tip3pfb_standard-Ce4+', 'tip3pfb_standard-U4+', 'tip3pfb_standard-Pu4+',
'tip3pfb_standard-Th4+', 'tip3p-fb-O', 'tip3p-fb-H', 'protein-C', 'protein-
CA', 'protein-CB', 'protein-CC', 'protein-CN', 'protein-CR', 'protein-CT',
'protein-CV', 'protein-CW', 'protein-C*', 'protein-CX', 'protein-H', 'protein-
HC', 'protein-H1', 'protein-HA', 'protein-H4', 'protein-H5', 'protein-HO',
'protein-HS', 'protein-HP', 'protein-N', 'protein-NA', 'protein-NB',
'protein-N2', 'protein-N3', 'protein-O', 'protein-O2', 'protein-OH',
'protein-S', 'protein-SH', 'protein-CO', 'protein-2C', 'protein-3C',
'protein-C8', 'DNA-C', 'DNA-CA', 'DNA-CB', 'DNA-CK', 'DNA-CM', 'DNA-CQ', 'DNA-
CT', 'DNA-H', 'DNA-HC', 'DNA-H1', 'DNA-H2', 'DNA-HA', 'DNA-H4', 'DNA-H5',
'DNA-HO', 'DNA-NA', 'DNA-NB', 'DNA-NC', 'DNA-N2', 'DNA-N*', 'DNA-O', 'DNA-O2',
'DNA-OH', 'DNA-OS', 'DNA-P', 'DNA-C7', 'DNA-C2', 'DNA-C1', 'DNA-CJ', 'RNA-C',
'RNA-CA', 'RNA-CB', 'RNA-CI', 'RNA-CP', 'RNA-CS', 'RNA-CQ', 'RNA-CT',
'RNA-C5', 'RNA-C4', 'RNA-H', 'RNA-H1', 'RNA-H2', 'RNA-HA', 'RNA-H4', 'RNA-H5',
'RNA-HO', 'RNA-NA', 'RNA-NB', 'RNA-NC', 'RNA-N2', 'RNA-N*', 'RNA-O', 'RNA-O2',
'RNA-OH', 'RNA-OS', 'RNA-P', 'cA', 'cB', 'cC', 'cD', 'hA', 'hB', 'hE', 'hL',
'hN', 'hO', 'hX', 'nA', 'oC', 'oH', 'oO', 'oP', 'oS', 'oT', 'pA', 'c', 'cs',
'c1', 'c2', 'c3', 'ca', 'cp', 'cq', 'cc', 'cd', 'ce', 'cf', 'cg', 'ch', 'cx',
'cy', 'c5', 'c6', 'cu', 'cv', 'cz', 'h1', 'h2', 'h3', 'h4', 'h5', 'ha', 'hc',
'hn', 'ho', 'hp', 'hs', 'hw', 'hx', 'f', 'cl', 'br', 'i', 'n', 'n1', 'n2',
'n3', 'n4', 'na', 'nb', 'nc', 'nd', 'ne', 'nf', 'nh', 'no', 'ns', 'nt', 'nx',
'ny', 'nz', 'n+', 'nu', 'nv', 'n7', 'n8', 'n9', 'ni', 'nj', 'nk', 'nl', 'nm',
'nn', 'np', 'nq', 'n5', 'n6', 'o', 'oh', 'op', 'oq', 'os', 'ow', 'p2', 'p3',
'p4', 'p5', 'pb', 'pc', 'pd', 'pe', 'pf', 'px', 'py', 's', 's2', 's4', 's6',
'sh', 'ss', 'sx', 'sy', 'sp', 'sq'])  
  
Exception: Could not find typename 'N' for atom '' in list of known atom
types.  
Known atom types are: dict_keys(['tip3pfb_standard-Li+', 'tip3pfb_standard-
Na+', 'tip3pfb_standard-K+', 'tip3pfb_standard-Rb+', 'tip3pfb_standard-Cs+',
'tip3pfb_standard-F-', 'tip3pfb_standard-Cl-', 'tip3pfb_standard-Br-',
'tip3pfb_standard-I-', 'tip3pfb_standard-Be2+', 'tip3pfb_standard-Cu2+',
'tip3pfb_standard-Ni2+', 'tip3pfb_standard-Pt2+', 'tip3pfb_standard-Zn2+',
'tip3pfb_standard-Co2+', 'tip3pfb_standard-Pd2+', 'tip3pfb_standard-Ag2+',
'tip3pfb_standard-Cr2+', 'tip3pfb_standard-Fe2+', 'tip3pfb_standard-Mg2+',
'tip3pfb_standard-V2+', 'tip3pfb_standard-Mn2+', 'tip3pfb_standard-Hg2+',
'tip3pfb_standard-Cd2+', 'tip3pfb_standard-Yb2+', 'tip3pfb_standard-Ca2+',
'tip3pfb_standard-Sn2+', 'tip3pfb_standard-Pb2+', 'tip3pfb_standard-Eu2+',
'tip3pfb_standard-Sr2+', 'tip3pfb_standard-Sm2+', 'tip3pfb_standard-Ba2+',
'tip3pfb_standard-Ra2+', 'tip3pfb_standard-Al3+', 'tip3pfb_standard-Fe3+',
'tip3pfb_standard-Cr3+', 'tip3pfb_standard-In3+', 'tip3pfb_standard-Tl3+',
'tip3pfb_standard-Y3+', 'tip3pfb_standard-La3+', 'tip3pfb_standard-Ce3+',
'tip3pfb_standard-Pr3+', 'tip3pfb_standard-Nd3+', 'tip3pfb_standard-Sm3+',
'tip3pfb_standard-Eu3+', 'tip3pfb_standard-Gd3+', 'tip3pfb_standard-Tb3+',
'tip3pfb_standard-Dy3+', 'tip3pfb_standard-Er3+', 'tip3pfb_standard-Tm3+',
'tip3pfb_standard-Lu3+', 'tip3pfb_standard-Hf4+', 'tip3pfb_standard-Zr4+',
'tip3pfb_standard-Ce4+', 'tip3pfb_standard-U4+', 'tip3pfb_standard-Pu4+',
'tip3pfb_standard-Th4+', 'tip3p-fb-O', 'tip3p-fb-H', 'protein-C', 'protein-
CA', 'protein-CB', 'protein-CC', 'protein-CN', 'protein-CR', 'protein-CT',
'protein-CV', 'protein-CW', 'protein-C*', 'protein-CX', 'protein-H', 'protein-
HC', 'protein-H1', 'protein-HA', 'protein-H4', 'protein-H5', 'protein-HO',
'protein-HS', 'protein-HP', 'protein-N', 'protein-NA', 'protein-NB',
'protein-N2', 'protein-N3', 'protein-O', 'protein-O2', 'protein-OH',
'protein-S', 'protein-SH', 'protein-CO', 'protein-2C', 'protein-3C',
'protein-C8', 'DNA-C', 'DNA-CA', 'DNA-CB', 'DNA-CK', 'DNA-CM', 'DNA-CQ', 'DNA-
CT', 'DNA-H', 'DNA-HC', 'DNA-H1', 'DNA-H2', 'DNA-HA', 'DNA-H4', 'DNA-H5',
'DNA-HO', 'DNA-NA', 'DNA-NB', 'DNA-NC', 'DNA-N2', 'DNA-N*', 'DNA-O', 'DNA-O2',
'DNA-OH', 'DNA-OS', 'DNA-P', 'DNA-C7', 'DNA-C2', 'DNA-C1', 'DNA-CJ', 'RNA-C',
'RNA-CA', 'RNA-CB', 'RNA-CI', 'RNA-CP', 'RNA-CS', 'RNA-CQ', 'RNA-CT',
'RNA-C5', 'RNA-C4', 'RNA-H', 'RNA-H1', 'RNA-H2', 'RNA-HA', 'RNA-H4', 'RNA-H5',
'RNA-HO', 'RNA-NA', 'RNA-NB', 'RNA-NC', 'RNA-N2', 'RNA-N*', 'RNA-O', 'RNA-O2',
'RNA-OH', 'RNA-OS', 'RNA-P', 'cA', 'cB', 'cC', 'cD', 'hA', 'hB', 'hE', 'hL',
'hN', 'hO', 'hX', 'nA', 'oC', 'oH', 'oO', 'oP', 'oS', 'oT', 'pA', 'c', 'cs',
'c1', 'c2', 'c3', 'ca', 'cp', 'cq', 'cc', 'cd', 'ce', 'cf', 'cg', 'ch', 'cx',
'cy', 'c5', 'c6', 'cu', 'cv', 'cz', 'h1', 'h2', 'h3', 'h4', 'h5', 'ha', 'hc',
'hn', 'ho', 'hp', 'hs', 'hw', 'hx', 'f', 'cl', 'br', 'i', 'n', 'n1', 'n2',
'n3', 'n4', 'na', 'nb', 'nc', 'nd', 'ne', 'nf', 'nh', 'no', 'ns', 'nt', 'nx',
'ny', 'nz', 'n+', 'nu', 'nv', 'n7', 'n8', 'n9', 'ni', 'nj', 'nk', 'nl', 'nm',
'nn', 'np', 'nq', 'n5', 'n6', 'o', 'oh', 'op', 'oq', 'os', 'ow', 'p2', 'p3',
'p4', 'p5', 'pb', 'pc', 'pd', 'pe', 'pf', 'px', 'py', 's', 's2', 's4', 's6',
'sh', 'ss', 'sx', 'sy', 'sp', 'sq'])  
  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\openmm\app\forcefield.py", line 1280, in createSystem  
raise Exception(msg)  
  
See log for complete Python traceback.  
  

> ui tool show "Add Hydrogens"

> addh

Summary of feedback from adding hydrogens to 10mer.pdb #1  
---  
notes | No usable SEQRES records for 10mer.pdb (#1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: /A HIS 1  
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: /A GLY 10  
1 hydrogen bonds  
/A GLY 10 is not terminus, removing H atom from 'C'  
0 hydrogens added  
  

> ui tool show "Build Structure"

> delete

Missing or invalid "atoms" argument: empty atom specifier  

> delete #1

[Repeated 1 time(s)]

> open C:/Users/jl80/Documents/10mer_2.pdb

Chain information for 10mer_2.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> hide cartoons

> show atoms

> minimize

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to 10mer_2.pdb #1  
---  
notes | No usable SEQRES records for 10mer_2.pdb (#1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: /A HIS 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A 11  
Chain-final residues that are not actual C termini:  
1 hydrogen bonds  
72 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue (net charge +0) with am1-bcc method  
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\jl80\AppData\Local\Temp\tmpgziymgss\ante.in.mol2 -fi mol2 -o
C:\Users\jl80\AppData\Local\Temp\tmpgziymgss\ante.out.mol2 -fo mol2 -c bcc -nc
0 -j 5 -s 2 -dr n  
() ``  
() `Welcome to antechamber 20.0: molecular input file processor.`  
() ``  
() `Info: Finished reading file
(C:\Users\jl80\AppData\Local\Temp\tmpgziymgss\ante.in.mol2); atoms read (9),
bonds read (8).`  
() `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
() `Running: "C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/bin/bondtype" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
() `bash.exe: warning: could not find /tmp, please create!`  
() ``  
() ``  
() `Running: "C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff`  
() `bash.exe: warning: could not find /tmp, please create!`  
() `Info: Total number of electrons: 32; net charge: 0`  
() ``  
() `Running: "C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out`  
() `bash.exe: warning: could not find /tmp, please create!`  
() ``  
() `Running: "C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/bin/am1bcc" -i ANTECHAMBER_AM1BCC_PRE.AC -o
ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
() `bash.exe: warning: could not find /tmp, please create!`  
() ``  
() `Running: "C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/bin/atomtype" -f ac -p bcc -o
ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
() `bash.exe: warning: could not find /tmp, please create!`  
() ``  
Charges for residue determined  
Dock prep finished  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 322, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 41, in cmd_minimize  
dock_prep_caller(session, [structure], memorize_name="minimization",
nogui=True,  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 146, in dock_prep_caller  
run_steps(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 107, in prep  
callback(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\addh\dock_prep.py", line 56, in run_for_dock_prep  
callback(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\add_charge\dock_prep.py", line 58, in run_for_dock_prep  
callback(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 156, in run_steps  
callback()  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 106, in <lambda>  
state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb())  
^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 43, in <lambda>  
steps=max_steps: _minimize(ses, struct, updates, log, steps), **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 216, in _minimize  
context = Context(system, integrator)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\openmm\openmm.py", line 5082, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
openmm.OpenMMException: Error compiling kernel: :204:24: warning: double
precision constant requires cl_khr_fp64, casting to single precision  
const real PI = (real) 3.14159265358979323846;  
^  
fcl build 1 succeeded.  
error: undefined reference to `_Z8atom_addPU3AS1mm()'  
  
error: midlevel compiler failed build.  
  
openmm.OpenMMException: Error compiling kernel: :204:24: warning: double
precision constant requires cl_khr_fp64, casting to single precision  
const real PI = (real) 3.14159265358979323846;  
^  
fcl build 1 succeeded.  
error: undefined reference to `_Z8atom_addPU3AS1mm()'  
  
error: midlevel compiler failed build.  
  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\openmm\openmm.py", line 5082, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> minimize

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to 10mer_2.pdb #1  
---  
notes | No usable SEQRES records for 10mer_2.pdb (#1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: /A HIS 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A 11  
Chain-final residues that are not actual C termini:  
1 hydrogen bonds  
0 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue (net charge +0) with am1-bcc method  
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\jl80\AppData\Local\Temp\tmpeet9863j\ante.in.mol2 -fi mol2 -o
C:\Users\jl80\AppData\Local\Temp\tmpeet9863j\ante.out.mol2 -fo mol2 -c bcc -nc
0 -j 5 -s 2 -dr n  
() ``  
() `Welcome to antechamber 20.0: molecular input file processor.`  
() ``  
() `Info: Finished reading file
(C:\Users\jl80\AppData\Local\Temp\tmpeet9863j\ante.in.mol2); atoms read (9),
bonds read (8).`  
() `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
() `Running: "C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/bin/bondtype" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
() `bash.exe: warning: could not find /tmp, please create!`  
() ``  
() ``  
() `Running: "C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff`  
() `bash.exe: warning: could not find /tmp, please create!`  
() `Info: Total number of electrons: 32; net charge: 0`  
() ``  
() `Running: "C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out`  
() `bash.exe: warning: could not find /tmp, please create!`  
() ``  
() `Running: "C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/bin/am1bcc" -i ANTECHAMBER_AM1BCC_PRE.AC -o
ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
() `bash.exe: warning: could not find /tmp, please create!`  
() ``  
() `Running: "C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/bin/atomtype" -f ac -p bcc -o
ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
() `bash.exe: warning: could not find /tmp, please create!`  
() ``  
Charges for residue determined  
Dock prep finished  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 322, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 41, in cmd_minimize  
dock_prep_caller(session, [structure], memorize_name="minimization",
nogui=True,  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 146, in dock_prep_caller  
run_steps(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 107, in prep  
callback(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\addh\dock_prep.py", line 56, in run_for_dock_prep  
callback(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\add_charge\dock_prep.py", line 58, in run_for_dock_prep  
callback(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 156, in run_steps  
callback()  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 106, in <lambda>  
state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb())  
^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 43, in <lambda>  
steps=max_steps: _minimize(ses, struct, updates, log, steps), **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 216, in _minimize  
context = Context(system, integrator)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\openmm\openmm.py", line 5082, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
openmm.OpenMMException: Error compiling kernel: :204:24: warning: double
precision constant requires cl_khr_fp64, casting to single precision  
const real PI = (real) 3.14159265358979323846;  
^  
fcl build 1 succeeded.  
error: undefined reference to `_Z8atom_addPU3AS1mm()'  
  
error: midlevel compiler failed build.  
  
openmm.OpenMMException: Error compiling kernel: :204:24: warning: double
precision constant requires cl_khr_fp64, casting to single precision  
const real PI = (real) 3.14159265358979323846;  
^  
fcl build 1 succeeded.  
error: undefined reference to `_Z8atom_addPU3AS1mm()'  
  
error: midlevel compiler failed build.  
  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\openmm\openmm.py", line 5082, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> minimize

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to 10mer_2.pdb #1  
---  
notes | No usable SEQRES records for 10mer_2.pdb (#1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: /A HIS 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A 11  
Chain-final residues that are not actual C termini:  
1 hydrogen bonds  
0 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue (net charge +0) with am1-bcc method  
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\jl80\AppData\Local\Temp\tmp7m5qkt_e\ante.in.mol2 -fi mol2 -o
C:\Users\jl80\AppData\Local\Temp\tmp7m5qkt_e\ante.out.mol2 -fo mol2 -c bcc -nc
0 -j 5 -s 2 -dr n  
() ``  
() `Welcome to antechamber 20.0: molecular input file processor.`  
() ``  
() `Info: Finished reading file
(C:\Users\jl80\AppData\Local\Temp\tmp7m5qkt_e\ante.in.mol2); atoms read (9),
bonds read (8).`  
() `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
() `Running: "C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/bin/bondtype" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
() `bash.exe: warning: could not find /tmp, please create!`  
() ``  
() ``  
() `Running: "C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff`  
() `bash.exe: warning: could not find /tmp, please create!`  
() `Info: Total number of electrons: 32; net charge: 0`  
() ``  
() `Running: "C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out`  
() `bash.exe: warning: could not find /tmp, please create!`  
() ``  
() `Running: "C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/bin/am1bcc" -i ANTECHAMBER_AM1BCC_PRE.AC -o
ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
() `bash.exe: warning: could not find /tmp, please create!`  
() ``  
() `Running: "C:/Program Files/ChimeraX
1.11.dev202509190047/bin/amber20/bin/atomtype" -f ac -p bcc -o
ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
() `bash.exe: warning: could not find /tmp, please create!`  
() ``  
Charges for residue determined  
Dock prep finished  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 322, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 41, in cmd_minimize  
dock_prep_caller(session, [structure], memorize_name="minimization",
nogui=True,  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 146, in dock_prep_caller  
run_steps(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 107, in prep  
callback(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\addh\dock_prep.py", line 56, in run_for_dock_prep  
callback(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\add_charge\dock_prep.py", line 58, in run_for_dock_prep  
callback(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 156, in run_steps  
callback()  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 106, in <lambda>  
state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb())  
^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 43, in <lambda>  
steps=max_steps: _minimize(ses, struct, updates, log, steps), **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 216, in _minimize  
context = Context(system, integrator)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\openmm\openmm.py", line 5082, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
openmm.OpenMMException: Error compiling kernel: :204:24: warning: double
precision constant requires cl_khr_fp64, casting to single precision  
const real PI = (real) 3.14159265358979323846;  
^  
fcl build 1 succeeded.  
error: undefined reference to `_Z8atom_addPU3AS1mm()'  
  
error: midlevel compiler failed build.  
  
openmm.OpenMMException: Error compiling kernel: :204:24: warning: double
precision constant requires cl_khr_fp64, casting to single precision  
const real PI = (real) 3.14159265358979323846;  
^  
fcl build 1 succeeded.  
error: undefined reference to `_Z8atom_addPU3AS1mm()'  
  
error: midlevel compiler failed build.  
  
File "C:\Program Files\ChimeraX 1.11.dev202509190047\bin\Lib\site-
packages\openmm\openmm.py", line 5082, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 10.18.10.4885
OpenGL renderer: Intel(R) HD Graphics
OpenGL vendor: Intel

Python: 3.11.9
Locale: en_US.cp65001
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows

Manufacturer: HP
Model: HP 15 Notebook PC
OS: Microsoft Windows 10 Home (Build 19045)
Memory: 4,179,574,784
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Pentium(R) CPU  N3540  @ 2.16GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.8.0
    build: 1.3.0
    certifi: 2025.8.3
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.3
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.0.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.16
    ChimeraX-AtomicLibrary: 14.2
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.dev202509190047
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7.1
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.17.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0.1
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.15.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.11
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.4
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.2.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.2
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.48.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.4.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.3
    comtypes: 1.4.11
    contourpy: 1.3.3
    coverage: 7.10.6
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.3
    debugpy: 1.8.17
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.60.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2025.4.15
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.7
    jedi: 0.19.2
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.1
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.5
    matplotlib-inline: 0.1.7
    msgpack: 1.1.1
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.12.1
    numpy: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.4.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.2.4
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 8.4.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pywin32: 311
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    requests: 2.32.4
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.2
    traitlets: 5.14.3
    typing_extensions: 4.15.0
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
    WMI: 1.5.1
File attachment: 10mer_2.pdb

10mer_2.pdb​

Attachments (1)

10mer_2.pdb​ (6.0 KB ) - added by cwa5555@… 7 weeks ago.
Added by email2trac

Download all attachments as: .zip

Change History (5)

by cwa5555@…, 7 weeks ago

Attachment: 10mer_2.pdb​ added

Added by email2trac

comment:1 by Eric Pettersen, 7 weeks ago

Cc: Tom Goddard added
Component: Unassigned → Structure Editing
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → OpenMM compiler failure on Windows

comment:2 by Eric Pettersen, 7 weeks ago

Hi Web,

Your structure minimizes fine in the daily build on my Mac. I don't have access to a Windows machine here at home, so it may not be until Thursday when I'm in the office again before I can investigate further.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by Tom Goddard, 7 weeks ago

The error message is your system OpenCL (GPU computing) driver saying it doesn't support double precision constants. I think OpenCL is part of your Intel graphics driver. ChimeraX reports you are using Intel HD graphics, driver version 10.18.10.4885 which is from 2017. You probably need a newer Intel graphics driver for OpenMM to work with OpenCL.

If the ChimeraX OpenMM minimization is using platform "OpenCL" by default on Window it may want to fallback to platform "CPU" if an OpenCL error occurs, or have a command option that allows the user to specify the platform as CPU or OpenCL or CUDA.

openmm.OpenMMException: Error compiling kernel: :204:24: warning: double
precision constant requires cl_khr_fp64, casting to single precision
const real PI = (real) 3.14159265358979323846;
fcl build 1 succeeded.
error: undefined reference to `_Z8atom_addPU3AS1mm()'

error: midlevel compiler failed build.

comment:4 by Eric Pettersen, 6 weeks ago

Resolution: → duplicate
Status: accepted → closed

Continued in #18869

Note: See TracTickets for help on using tickets.