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Opened 7 weeks ago
Last modified 2 weeks ago
#19151 accepted defect
Various minimize errors
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.11.dev202510140238 (2025-10-14 02:38:50 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
Startup Messages
---
note | Updated animation length to 0:05.00
UCSF ChimeraX version: 1.11.dev202510140238 (2025-10-14)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/alex_/Downloads/Proyecto/Dianas originales/8CGC.pdb"
8CGC.pdb title:
Structure of CSF1R In complex with A pyrollopyrimidine (compound 23) [more
info...]
Chain information for 8CGC.pdb #1
---
Chain | Description | UniProt
A | macrophage colony-stimulating factor 1 receptor | CSF1R_HUMAN 542-919
Non-standard residues in 8CGC.pdb #1
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
LMR — (2S)-2-hydroxybutanedioic acid (L-malate)
UIK —
[4-[4-[methyl-[(3-methylphenyl)methyl]amino]-7~{H}-pyrrolo[2,3-D]pyrimidin-6-yl]phenyl]methanol
84 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> delete solvent
> delete ligand
> addh
Summary of feedback from adding hydrogens to 8CGC.pdb #1
---
notes | Termini for 8CGC.pdb (#1) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A GLN 547, /A GLY 747
Chain-final residues that are actual C termini: /A ARG 919
Chain-final residues that are not actual C termini: /A GLY 684
307 hydrogen bonds
Adding 'H' to /A GLN 547
Adding 'H' to /A GLY 747
2449 hydrogens added
> addcharge
Using Amber 20 recommended default charges and atom types for standard
residues
> minimize
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Summary of feedback from adding hydrogens to 8CGC.pdb #1
---
notes | Termini for 8CGC.pdb (#1) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A GLN 547, /A GLY 747
Chain-final residues that are actual C termini: /A ARG 919
Chain-final residues that are not actual C termini: /A GLY 684
294 hydrogen bonds
0 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
Dock prep finished
> save "C:/Users/alex_/Downloads/Proyecto/Dianas limpias/8CGC.pdb"
> close
> open "C:/Users/alex_/Downloads/Proyecto/Dianas originales/6IG8.pdb"
6IG8.pdb title:
Crystal structure of CSF-1R kinase domain with A small molecular inhibitor,
jte-952 [more info...]
Chain information for 6IG8.pdb #1
---
Chain | Description | UniProt
A | macrophage colony-stimulating factor 1 receptor | CSF1R_HUMAN 550-695 742-919
Non-standard residues in 6IG8.pdb #1
---
A7O —
(3-{4-[(4-cyclopropylphenyl)methoxy]-3-methoxyphenyl}azetidin-1-yl)(4-{[(2S)-2,3-dihydroxypropoxy]methyl}pyridin-2-yl)methanone
GOL — glycerol (glycerin; propane-1,2,3-triol)
MG — magnesium ion
117 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> delete solvent delete ligand
Expected a keyword
> delete solvent
[Repeated 1 time(s)]
> delete ligand
> addh
Summary of feedback from adding hydrogens to 6IG8.pdb #1
---
notes | Termini for 6IG8.pdb (#1) chain A determined from SEQRES records
Chain-initial residues that are actual N termini: /A TRP 550
Chain-initial residues that are not actual N termini: /A THR 562, /A GLY 747
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A GLU 554, /A LEU 687, /A
GLU 916
296 hydrogen bonds
Adding 'H' to /A THR 562
Adding 'H' to /A GLY 747
/A GLU 916 is not terminus, removing H atom from 'C'
2371 hydrogens added
> addcharge
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue MG (net charge +2) with am1-bcc method
> minimize
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Summary of feedback from adding hydrogens to 6IG8.pdb #1
---
notes | Termini for 6IG8.pdb (#1) chain A determined from SEQRES records
Chain-initial residues that are actual N termini: /A TRP 550
Chain-initial residues that are not actual N termini: /A THR 562, /A GLY 747
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A GLU 554, /A LEU 687, /A
GLU 916
283 hydrogen bonds
/A GLU 916 is not terminus, removing H atom from 'C'
0 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue MG (net charge +2) with am1-bcc method
Dock prep finished
> save "C:/Users/alex_/Downloads/Proyecto/Dianas limpias/6IG8.pdb"
> close
> open "C:/Users/alex_/Downloads/Proyecto/Dianas originales/5GPG.pdb"
5GPG.pdb title:
Co-crystal structure of the FK506 binding domain of human FKBP25, rapamycin
and the FRB domain of human mtor [more info...]
Chain information for 5GPG.pdb #1
---
Chain | Description | UniProt
A | peptidyl-prolyl cis-trans isomerase FKBP3 | FKBP3_HUMAN 109-224
B | serine/threonine-protein kinase mtor | MTOR_HUMAN 2021-2112
Non-standard residues in 5GPG.pdb #1
---
RAP — rapamycin immunosuppressant drug
> delete solvent
[Repeated 1 time(s)]
> delete ligand
> addh
Summary of feedback from adding hydrogens to 5GPG.pdb #1
---
warning | Unknown hybridization for atom (AS) of residue type CAS; not adding hydrogens to it
notes | Termini for 5GPG.pdb (#1) chain A determined from SEQRES records
Termini for 5GPG.pdb (#1) chain B determined from SEQRES records
Chain-initial residues that are actual N termini: /A SER 108, /B SER 2020
Chain-initial residues that are not actual N termini: /A ASN 158
Chain-final residues that are actual C termini: /A ASP 224, /B SER 2112
Chain-final residues that are not actual C termini: /A GLN 150
Missing OXT added to C-terminal residue /A ASP 224
Missing OXT added to C-terminal residue /B SER 2112
198 hydrogen bonds
Adding 'H' to /A ASN 158
1640 hydrogens added
> addcharge
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue CAS (net charge +0) with am1-bcc method
Atom whose IDATM type has no equivalent Sybyl type: /? CAS 1 As1 (type: As)
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\TEMP~1.DES\AppData\Local\Temp\tmp3zxtk0j0\ante.in.mol2 -fi mol2 -o
C:\Users\TEMP~1.DES\AppData\Local\Temp\tmp3zxtk0j0\ante.out.mol2 -fo mol2 -c
bcc -nc 0 -j 5 -s 2 -dr n
(CAS) ``
(CAS) `Welcome to antechamber 20.0: molecular input file processor.`
(CAS) ``
(CAS) `Info: Finished reading file
(C:\Users\TEMP~1.DES\AppData\Local\Temp\tmp3zxtk0j0\ante.in.mol2); atoms read
(31), bonds read (30).`
(CAS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(CAS) `Running: "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/bondtype" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(CAS) `bash.exe: warning: could not find /tmp, please create!`
(CAS) `Warning: For atom (ID: 7, Name: As1) the best APS is not zero.`
(CAS) ` Bonds involving this atom are frozen.`
(CAS) ``
(CAS) ``
(CAS) `Running: "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff`
(CAS) `bash.exe: warning: could not find /tmp, please create!`
(CAS) `Info: Total number of electrons: 144; net charge: 0`
(CAS) ``
(CAS) `Running: "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out`
(CAS) `bash.exe: warning: could not find /tmp, please create!`
(CAS) `/usr/bin/antechamber: Fatal Error!`
(CAS) `Cannot properly run ""C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out".`
Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
QMMM: Atom number: 7 has atomic number 33.
QMMM: There are no AM1 parameters for this element. Sorry.
SANDER BOMB in subroutine qm2_load_params_and_allocate
UNSUPPORTED ELEMENT
QM AM1 NOT AVAILABLE FOR THIS ATOM
Failure running ANTECHAMBER for residue CAS
Check reply log for details
> minimize
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Summary of feedback from adding hydrogens to 5GPG.pdb #1
---
warning | Unknown hybridization for atom (AS) of residue type CAS; not adding hydrogens to it
notes | Termini for 5GPG.pdb (#1) chain A determined from SEQRES records
Termini for 5GPG.pdb (#1) chain B determined from SEQRES records
Chain-initial residues that are actual N termini: /A SER 108, /B SER 2020
Chain-initial residues that are not actual N termini: /A ASN 158
Chain-final residues that are actual C termini: /A ASP 224, /B SER 2112
Chain-final residues that are not actual C termini: /A GLN 150
192 hydrogen bonds
0 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue CAS (net charge +0) with am1-bcc method
Atom whose IDATM type has no equivalent Sybyl type: /? CAS 1 As1 (type: As)
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\TEMP~1.DES\AppData\Local\Temp\tmppy6jxu0w\ante.in.mol2 -fi mol2 -o
C:\Users\TEMP~1.DES\AppData\Local\Temp\tmppy6jxu0w\ante.out.mol2 -fo mol2 -c
bcc -nc 0 -j 5 -s 2 -dr n
(CAS) ``
(CAS) `Welcome to antechamber 20.0: molecular input file processor.`
(CAS) ``
(CAS) `Info: Finished reading file
(C:\Users\TEMP~1.DES\AppData\Local\Temp\tmppy6jxu0w\ante.in.mol2); atoms read
(31), bonds read (30).`
(CAS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(CAS) `Running: "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/bondtype" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(CAS) `bash.exe: warning: could not find /tmp, please create!`
(CAS) `Warning: For atom (ID: 7, Name: As1) the best APS is not zero.`
(CAS) ` Bonds involving this atom are frozen.`
(CAS) ``
(CAS) ``
(CAS) `Running: "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff`
(CAS) `bash.exe: warning: could not find /tmp, please create!`
(CAS) `Info: Total number of electrons: 144; net charge: 0`
(CAS) ``
(CAS) `Running: "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out`
(CAS) `bash.exe: warning: could not find /tmp, please create!`
(CAS) `/usr/bin/antechamber: Fatal Error!`
(CAS) `Cannot properly run ""C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out".`
Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
QMMM: Atom number: 7 has atomic number 33.
QMMM: There are no AM1 parameters for this element. Sorry.
SANDER BOMB in subroutine qm2_load_params_and_allocate
UNSUPPORTED ELEMENT
QM AM1 NOT AVAILABLE FOR THIS ATOM
Failure running ANTECHAMBER for residue CAS
Check reply log for details
> save "C:/Users/alex_/Downloads/Proyecto/Dianas limpias/5GPG.pdb"
> close
> open "C:/Users/alex_/Downloads/Proyecto/Dianas originales/4DRJ.pdb"
4DRJ.pdb title:
O-crystal structure of the ppiase domain of FKBP52, rapamycin and the FRB
fragment of mtor [more info...]
Chain information for 4DRJ.pdb #1
---
Chain | Description | UniProt
A | peptidyl-prolyl cis-trans isomerase FKBP4 | FKBP4_HUMAN 1-140
B | serine/threonine-protein kinase mtor | MTOR_HUMAN 2025-2114
Non-standard residues in 4DRJ.pdb #1
---
RAP — rapamycin immunosuppressant drug
SO4 — sulfate ion
26 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
1770 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> delete solvent
> delete ligand
> addh
Summary of feedback from adding hydrogens to 4DRJ.pdb #1
---
warnings | Not adding hydrogens to /A GLU 21 CB because it is missing heavy-atom bond partners
Not adding hydrogens to /A ASP 72 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A ARG 73 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LYS 74 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A ASP 75 CB because it is missing heavy-atom bond
partners
8 messages similar to the above omitted
notes | Termini for 4DRJ.pdb (#1) chain A determined from SEQRES records
Termini for 4DRJ.pdb (#1) chain B determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A PRO 19, /B MET 2019
Chain-final residues that are actual C termini: /B GLN 2114
Chain-final residues that are not actual C termini: /A GLY 139
209 hydrogen bonds
Adding 'H' to /B MET 2019
/A GLY 139 is not terminus, removing H atom from 'C'
1631 hydrogens added
> addcharge
Using Amber 20 recommended default charges and atom types for standard
residues
1 structure has non-integral total charge.
Details in log.
Here are the structures will non-integral total charge along with the
particular residues from those structures with non-integral total charge:
4DRJ.pdb #1: /A GLU 21: -0.0618, /A ASP 72: -0.1722, /A ARG 73: -0.0369, /A
LYS 74: -0.0353, /A ASP 75: -0.1722, /B GLU 2022: -0.0618, /B GLU 2025:
-0.0618, /B GLU 2029: -0.0618, /B LEU 2065: -0.1842, /B THR 2068: 0.3128, /B
SER 2069: 0.1567, /B GLN 2072: -0.0361, and /B LYS 2095: -0.0353
> minimize
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Filling out missing side chains
/A GLU 21: phi -127.2, psi 79.9 trans
/A ASP 72: phi -91.9, psi 14.6 trans
/A ARG 73: phi -105.8, psi 152.2 trans
/A LYS 74: phi -76.7, psi -16.0 trans
/A ASP 75: phi -128.6, psi 153.1 trans
/B GLU 2022: phi -58.8, psi -49.3 trans
/B GLU 2025: phi -65.2, psi -48.0 trans
/B GLU 2029: phi -63.0, psi -41.7 trans
/B LEU 2065: phi -49.8, psi -51.8 trans
/B THR 2068: phi -57.1, psi -41.2 trans
/B SER 2069: phi -57.8, psi -46.0 trans
/B GLN 2072: phi -56.0, psi -44.3 trans
/B LYS 2095: phi -56.0, psi -31.5 trans
Applying GLU rotamer (chi angles: 66.6 -84.2 17.3) to /A GLU 21
Applying ASP rotamer (chi angles: 64.3 -2.2) to /A ASP 72
Applying ARG rotamer (chi angles: -60.7 -71.9 85.6 -168.5) to /A ARG 73
Applying LYS rotamer (chi angles: -85.2 77.0 -84.3 177.6) to /A LYS 74
Applying ASP rotamer (chi angles: 64.6 83.2) to /A ASP 75
Applying GLU rotamer (chi angles: -67.4 80.8 1.3) to /B GLU 2022
Applying GLU rotamer (chi angles: -177.8 177.5 -1.2) to /B GLU 2025
Applying GLU rotamer (chi angles: -69.9 176.8 -8.7) to /B GLU 2029
Applying LEU rotamer (chi angles: 178.4 62.6) to /B LEU 2065
Applying THR rotamer (chi angles: 58.7) to /B THR 2068
Applying SER rotamer (chi angles: -65.7) to /B SER 2069
Applying GLN rotamer (chi angles: -175.4 64.8 78.1) to /B GLN 2072
Applying LYS rotamer (chi angles: 69.3 179.7 177.3 64.0) to /B LYS 2095
Summary of feedback from adding hydrogens to 4DRJ.pdb #1
---
notes | Termini for 4DRJ.pdb (#1) chain A determined from SEQRES records
Termini for 4DRJ.pdb (#1) chain B determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A PRO 19, /B MET 2019
Chain-final residues that are actual C termini: /B GLN 2114
Chain-final residues that are not actual C termini: /A GLY 139
206 hydrogen bonds
/A GLY 139 is not terminus, removing H atom from 'C'
76 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
Dock prep finished
> save "C:/Users/alex_/Downloads/Proyecto/Dianas limpias/4DRJ.pdb"
> close
> open "C:/Users/alex_/Downloads/Proyecto/Dianas originales/6N7A.pdb"
6N7A.pdb title:
Structure of the human JAK1 kinase domain with compound 39 [more info...]
Chain information for 6N7A.pdb #1
---
Chain | Description | UniProt
A B | tyrosine-protein kinase JAK1 | JAK1_HUMAN 854-1154
Non-standard residues in 6N7A.pdb #1
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
KEV —
N-[3-(5-chloro-2-methoxyphenyl)-1-methyl-1H-pyrazol-4-yl]-2-methyl-2H-pyrazolo[4,3-C]pyridine-7-carboxamide
34 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> delete solvent
> delete ligand
> addh
Summary of feedback from adding hydrogens to 6N7A.pdb #1
---
warnings | Not adding hydrogens to /A LYS 1038 CB because it is missing heavy-atom bond partners
Not adding hydrogens to /A ARG 1041 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /B LYS 859 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /B LYS 860 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /B GLU 864 CB because it is missing heavy-atom bond
partners
3 messages similar to the above omitted
notes | Termini for 6N7A.pdb (#1) chain A determined from SEQRES records
Termini for 6N7A.pdb (#1) chain B determined from SEQRES records
Chain-initial residues that are actual N termini: /B GLY 851
Chain-initial residues that are not actual N termini: /A VAL 865, /A HIS 918,
/A GLY 951, /A HIS 1096, /B HIS 918, /B GLY 951
Chain-final residues that are actual C termini: /A LYS 1154, /B LYS 1154
Chain-final residues that are not actual C termini: /A PRO 912, /A THR 945, /A
GLY 1093, /B PRO 912, /B THR 945
Missing OXT added to C-terminal residue /A LYS 1154
Missing OXT added to C-terminal residue /B LYS 1154
576 hydrogen bonds
Adding 'H' to /A VAL 865
Adding 'H' to /A HIS 918
Adding 'H' to /A GLY 951
Adding 'H' to /A HIS 1096
Adding 'H' to /B HIS 918
1 messages similar to the above omitted
4581 hydrogens added
> addcharge
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue PTR+PTR (net charge -4) with am1-bcc
method
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\TEMP~1.DES\AppData\Local\Temp\tmpd7w0b8r8\ante.in.mol2 -fi mol2 -o
C:\Users\TEMP~1.DES\AppData\Local\Temp\tmpd7w0b8r8\ante.out.mol2 -fo mol2 -c
bcc -nc -4 -j 5 -s 2 -dr n
(PTR+PTR) ``
(PTR+PTR) `Welcome to antechamber 20.0: molecular input file processor.`
(PTR+PTR) ``
(PTR+PTR) `Info: Finished reading file
(C:\Users\TEMP~1.DES\AppData\Local\Temp\tmpd7w0b8r8\ante.in.mol2); atoms read
(60), bonds read (61).`
(PTR+PTR) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(PTR+PTR) `Running: "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/bondtype" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(PTR+PTR) `bash.exe: warning: could not find /tmp, please create!`
(PTR+PTR) ``
(PTR+PTR) ``
(PTR+PTR) `Running: "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff`
(PTR+PTR) `bash.exe: warning: could not find /tmp, please create!`
(PTR+PTR) `Info: Total number of electrons: 292; net charge: -4`
(PTR+PTR) ``
(PTR+PTR) `Running: "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out`
(PTR+PTR) `bash.exe: warning: could not find /tmp, please create!`
(PTR+PTR) ``
(PTR+PTR) `Running: "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/am1bcc" -i ANTECHAMBER_AM1BCC_PRE.AC -o
ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`
(PTR+PTR) `bash.exe: warning: could not find /tmp, please create!`
(PTR+PTR) ``
(PTR+PTR) `Running: "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/atomtype" -f ac -p bcc -o
ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(PTR+PTR) `bash.exe: warning: could not find /tmp, please create!`
(PTR+PTR) ``
Charges for residue PTR+PTR determined
1 structure has non-integral total charge.
Details in log.
Here are the structures will non-integral total charge along with the
particular residues from those structures with non-integral total charge:
6N7A.pdb #1: /A PTR 1034: -1.9885, /A PTR 1035: -2.0115, /A LYS 1038: -0.0353,
/A ARG 1041: -0.0369, /B LYS 859: -0.0353, /B LYS 860: -0.0353, /B GLU 864:
-0.0618, /B PTR 1034: -1.9885, /B PTR 1035: -2.0115, /B LYS 1038: -0.0353, /B
ARG 1041: -0.0369, and /B ASP 1042: -0.1722
> minimize
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Filling out missing side chains
/A LYS 1038: phi -117.8, psi 112.6 trans
/A ARG 1041: phi -67.8, psi 150.4 trans
/B LYS 859: phi -98.8, psi 95.5 trans
/B LYS 860: phi -76.8, psi 140.7 trans
/B GLU 864: phi -101.3, psi 118.7 trans
/B LYS 1038: phi -79.5, psi -42.4 trans
/B ARG 1041: phi -54.4, psi -60.7 trans
/B ASP 1042: phi -94.8, psi 65.8 trans
Applying LYS rotamer (chi angles: -178.6 170.5 70.9 174.1) to /A LYS 1038
Applying ARG rotamer (chi angles: -68.0 177.9 -66.7 172.0) to /A ARG 1041
Applying LYS rotamer (chi angles: -179.9 69.8 177.9 68.4) to /B LYS 859
Applying LYS rotamer (chi angles: -65.4 -177.3 -176.9 -64.6) to /B LYS 860
Applying GLU rotamer (chi angles: 67.1 -82.6 40.1) to /B GLU 864
Applying LYS rotamer (chi angles: -86.0 68.0 178.6 178.3) to /B LYS 1038
Applying ARG rotamer (chi angles: -71.3 -178.3 -70.2 168.1) to /B ARG 1041
Applying ASP rotamer (chi angles: -171.9 9.7) to /B ASP 1042
Summary of feedback from adding hydrogens to 6N7A.pdb #1
---
notes | Termini for 6N7A.pdb (#1) chain A determined from SEQRES records
Termini for 6N7A.pdb (#1) chain B determined from SEQRES records
Chain-initial residues that are actual N termini: /B GLY 851
Chain-initial residues that are not actual N termini: /A VAL 865, /A HIS 918,
/A GLY 951, /A HIS 1096, /B HIS 918, /B GLY 951
Chain-final residues that are actual C termini: /A LYS 1154, /B LYS 1154
Chain-final residues that are not actual C termini: /A PRO 912, /A THR 945, /A
GLY 1093, /B PRO 912, /B THR 945
564 hydrogen bonds
72 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue PTR+PTR (net charge -4) with am1-bcc
method
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\TEMP~1.DES\AppData\Local\Temp\tmpj0vw3pky\ante.in.mol2 -fi mol2 -o
C:\Users\TEMP~1.DES\AppData\Local\Temp\tmpj0vw3pky\ante.out.mol2 -fo mol2 -c
bcc -nc -4 -j 5 -s 2 -dr n
(PTR+PTR) ``
(PTR+PTR) `Welcome to antechamber 20.0: molecular input file processor.`
(PTR+PTR) ``
(PTR+PTR) `Info: Finished reading file
(C:\Users\TEMP~1.DES\AppData\Local\Temp\tmpj0vw3pky\ante.in.mol2); atoms read
(60), bonds read (61).`
(PTR+PTR) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(PTR+PTR) `Running: "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/bondtype" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(PTR+PTR) `bash.exe: warning: could not find /tmp, please create!`
(PTR+PTR) ``
(PTR+PTR) ``
(PTR+PTR) `Running: "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff`
(PTR+PTR) `bash.exe: warning: could not find /tmp, please create!`
(PTR+PTR) `Info: Total number of electrons: 292; net charge: -4`
(PTR+PTR) ``
(PTR+PTR) `Running: "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out`
(PTR+PTR) `bash.exe: warning: could not find /tmp, please create!`
(PTR+PTR) ``
(PTR+PTR) `Running: "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/am1bcc" -i ANTECHAMBER_AM1BCC_PRE.AC -o
ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`
(PTR+PTR) `bash.exe: warning: could not find /tmp, please create!`
(PTR+PTR) ``
(PTR+PTR) `Running: "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/atomtype" -f ac -p bcc -o
ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(PTR+PTR) `bash.exe: warning: could not find /tmp, please create!`
(PTR+PTR) ``
Charges for residue PTR+PTR determined
Dock prep finished
> save "C:/Users/alex_/Downloads/Proyecto/Dianas limpias/6N7A.pdb"
> close
> open "C:/Users/alex_/Downloads/Proyecto/Dianas originales/6PNG.pdb"
6PNG.pdb title:
Structure of human neuronal nitric oxide synthase R354A/G357D mutant heme
domain In complex with 7-(3-(aminomethyl)-4-propoxyphenyl)-4-
methylquinolin-2-amine [more info...]
Chain information for 6PNG.pdb #1
---
Chain | Description | UniProt
A B | nitric oxide synthase, brain | NOS1_HUMAN 302-722
Non-standard residues in 6PNG.pdb #1
---
HEM — protoporphyrin IX containing Fe (HEME)
OSG — 7-[3-(aminomethyl)-4-propoxyphenyl]-4-methylquinolin-2-amine
ZN — zinc ion
18 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
6696 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> delete solvent
> delete ligand
> addh
Summary of feedback from adding hydrogens to 6PNG.pdb #1
---
notes | Termini for 6PNG.pdb (#1) chain A determined from SEQRES records
Termini for 6PNG.pdb (#1) chain B determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A PRO 303, /A ASP 352,
/B ARG 304, /B ALA 354
Chain-final residues that are actual C termini: /A LYS 722, /B LYS 722
Chain-final residues that are not actual C termini: /A PRO 343, /B PRO 343
769 hydrogen bonds
Adding 'H' to /A ASP 352
Adding 'H' to /B ARG 304
Adding 'H' to /B ALA 354
6520 hydrogens added
> addcharge
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue HEM (net charge +2) with am1-bcc method
Assigning partial charges to residue ZN (net charge +2) with am1-bcc method
> minimize
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Summary of feedback from adding hydrogens to 6PNG.pdb #1
---
notes | Termini for 6PNG.pdb (#1) chain A determined from SEQRES records
Termini for 6PNG.pdb (#1) chain B determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A PRO 303, /A ASP 352,
/B ARG 304, /B ALA 354
Chain-final residues that are actual C termini: /A LYS 722, /B LYS 722
Chain-final residues that are not actual C termini: /A PRO 343, /B PRO 343
747 hydrogen bonds
0 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue HEM (net charge +2) with am1-bcc method
Assigning partial charges to residue ZN (net charge +2) with am1-bcc method
Dock prep finished
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.11.dev202510140238\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 322, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.11.dev202510140238\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.dev202510140238\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.dev202510140238\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.dev202510140238\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.dev202510140238\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 107, in prep
callback(session, state, structures)
File "C:\Program Files\ChimeraX 1.11.dev202510140238\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.dev202510140238\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.dev202510140238\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.dev202510140238\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.dev202510140238\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 156, in run_steps
callback()
File "C:\Program Files\ChimeraX 1.11.dev202510140238\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.dev202510140238\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.dev202510140238\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 144, in _minimize
templates, no_tmpl_omm_residues =
forcefield.generateTemplatesForUnmatchedResidues(top)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.dev202510140238\bin\Lib\site-
packages\openmm\app\forcefield.py", line 1166, in
generateTemplatesForUnmatchedResidues
unmatched_residues = self.getUnmatchedResidues(topology)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.dev202510140238\bin\Lib\site-
packages\openmm\app\forcefield.py", line 1105, in getUnmatchedResidues
[template, matches] = self._getResidueTemplateMatches(res, bondedToAtom)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.dev202510140238\bin\Lib\site-
packages\openmm\app\forcefield.py", line 1045, in _getResidueTemplateMatches
raise Exception('Multiple non-identical matching templates found for residue
%d (%s): %s.' % (res.index+1, res.name, ', '.join(match[0].name for match in
allMatches)))
Exception: Multiple non-identical matching templates found for residue 822
(HEM): FE, FE2.
Exception: Multiple non-identical matching templates found for residue 822
(HEM): FE, FE2.
File "C:\Program Files\ChimeraX 1.11.dev202510140238\bin\Lib\site-
packages\openmm\app\forcefield.py", line 1045, in _getResidueTemplateMatches
raise Exception('Multiple non-identical matching templates found for residue
%d (%s): %s.' % (res.index+1, res.name, ', '.join(match[0].name for match in
allMatches)))
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 6PNG.pdb #1
---
notes | Termini for 6PNG.pdb (#1) chain A determined from SEQRES records
Termini for 6PNG.pdb (#1) chain B determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A PRO 303, /A ASP 352,
/B ARG 304, /B ALA 354
Chain-final residues that are actual C termini: /A LYS 722, /B LYS 722
Chain-final residues that are not actual C termini: /A PRO 343, /B PRO 343
747 hydrogen bonds
0 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue HEM (net charge +2) with am1-bcc method
Assigning partial charges to residue ZN (net charge +2) with am1-bcc method
Dock prep finished
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.11.dev202510140238\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 322, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.11.dev202510140238\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.dev202510140238\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.dev202510140238\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.dev202510140238\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.dev202510140238\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 107, in prep
callback(session, state, structures)
File "C:\Program Files\ChimeraX 1.11.dev202510140238\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.dev202510140238\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.dev202510140238\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.dev202510140238\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.dev202510140238\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 156, in run_steps
callback()
File "C:\Program Files\ChimeraX 1.11.dev202510140238\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.dev202510140238\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.dev202510140238\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 144, in _minimize
templates, no_tmpl_omm_residues =
forcefield.generateTemplatesForUnmatchedResidues(top)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.dev202510140238\bin\Lib\site-
packages\openmm\app\forcefield.py", line 1166, in
generateTemplatesForUnmatchedResidues
unmatched_residues = self.getUnmatchedResidues(topology)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.dev202510140238\bin\Lib\site-
packages\openmm\app\forcefield.py", line 1105, in getUnmatchedResidues
[template, matches] = self._getResidueTemplateMatches(res, bondedToAtom)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.dev202510140238\bin\Lib\site-
packages\openmm\app\forcefield.py", line 1045, in _getResidueTemplateMatches
raise Exception('Multiple non-identical matching templates found for residue
%d (%s): %s.' % (res.index+1, res.name, ', '.join(match[0].name for match in
allMatches)))
Exception: Multiple non-identical matching templates found for residue 822
(HEM): FE, FE2.
Exception: Multiple non-identical matching templates found for residue 822
(HEM): FE, FE2.
File "C:\Program Files\ChimeraX 1.11.dev202510140238\bin\Lib\site-
packages\openmm\app\forcefield.py", line 1045, in _getResidueTemplateMatches
raise Exception('Multiple non-identical matching templates found for residue
%d (%s): %s.' % (res.index+1, res.name, ', '.join(match[0].name for match in
allMatches)))
See log for complete Python traceback.
> save "C:/Users/alex_/Downloads/Proyecto/Dianas limpias/6PNG.pdb"
> close
> open "C:/Users/alex_/Downloads/Proyecto/Dianas originales/8UFP.pdb"
8UFP.pdb title:
Structure of human neuronal nitric oxide synthase R354A/G357D mutant heme
domain In complex with 4-methyl-7-(4-methyl-2,3,4,5-
tetrahydrobenzo[F][1,4]oxazepin-7-yl)quinolin-2-amine dihydrochloride [more
info...]
Chain information for 8UFP.pdb #1
---
Chain | Description | UniProt
A B | nitric oxide synthase, brain | NOS1_HUMAN 302-722
Non-standard residues in 8UFP.pdb #1
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
HEM — protoporphyrin IX containing Fe (HEME)
WK2 —
(7M)-4-methyl-7-(4-methyl-2,3,4,5-tetrahydro-1,4-benzoxazepin-7-yl)quinolin-2-amine
ZN — zinc ion
44 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
6740 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> delete solvent
> delete ligand
> addh
Summary of feedback from adding hydrogens to 8UFP.pdb #1
---
notes | Termini for 8UFP.pdb (#1) chain A determined from SEQRES records
Termini for 8UFP.pdb (#1) chain B determined from SEQRES records
Chain-initial residues that are actual N termini: /A CYS 302
Chain-initial residues that are not actual N termini: /A ARG 349, /B ARG 304,
/B VAL 353
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A PRO 343, /A LYS 722, /B
SER 344, /B LYS 722
774 hydrogen bonds
Adding 'H' to /A ARG 349
Adding 'H' to /B ARG 304
Adding 'H' to /B VAL 353
/A LYS 722 is not terminus, removing H atom from 'C'
/B LYS 722 is not terminus, removing H atom from 'C'
6568 hydrogens added
> addcharge
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue HEM (net charge +2) with am1-bcc method
Assigning partial charges to residue ZN (net charge +2) with am1-bcc method
> minimize
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Summary of feedback from adding hydrogens to 8UFP.pdb #1
---
notes | Termini for 8UFP.pdb (#1) chain A determined from SEQRES records
Termini for 8UFP.pdb (#1) chain B determined from SEQRES records
Chain-initial residues that are actual N termini: /A CYS 302
Chain-initial residues that are not actual N termini: /A ARG 349, /B ARG 304,
/B VAL 353
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A PRO 343, /A LYS 722, /B
SER 344, /B LYS 722
746 hydrogen bonds
/A LYS 722 is not terminus, removing H atom from 'C'
/B LYS 722 is not terminus, removing H atom from 'C'
0 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue HEM (net charge +2) with am1-bcc method
Assigning partial charges to residue ZN (net charge +2) with am1-bcc method
Dock prep finished
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.11.dev202510140238\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 322, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.11.dev202510140238\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.dev202510140238\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.dev202510140238\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.dev202510140238\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.dev202510140238\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 107, in prep
callback(session, state, structures)
File "C:\Program Files\ChimeraX 1.11.dev202510140238\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.dev202510140238\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.dev202510140238\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.dev202510140238\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.dev202510140238\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 156, in run_steps
callback()
File "C:\Program Files\ChimeraX 1.11.dev202510140238\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.dev202510140238\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.dev202510140238\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 144, in _minimize
templates, no_tmpl_omm_residues =
forcefield.generateTemplatesForUnmatchedResidues(top)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.dev202510140238\bin\Lib\site-
packages\openmm\app\forcefield.py", line 1166, in
generateTemplatesForUnmatchedResidues
unmatched_residues = self.getUnmatchedResidues(topology)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.dev202510140238\bin\Lib\site-
packages\openmm\app\forcefield.py", line 1105, in getUnmatchedResidues
[template, matches] = self._getResidueTemplateMatches(res, bondedToAtom)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.dev202510140238\bin\Lib\site-
packages\openmm\app\forcefield.py", line 1045, in _getResidueTemplateMatches
raise Exception('Multiple non-identical matching templates found for residue
%d (%s): %s.' % (res.index+1, res.name, ', '.join(match[0].name for match in
allMatches)))
Exception: Multiple non-identical matching templates found for residue 828
(HEM): FE, FE2.
Exception: Multiple non-identical matching templates found for residue 828
(HEM): FE, FE2.
File "C:\Program Files\ChimeraX 1.11.dev202510140238\bin\Lib\site-
packages\openmm\app\forcefield.py", line 1045, in _getResidueTemplateMatches
raise Exception('Multiple non-identical matching templates found for residue
%d (%s): %s.' % (res.index+1, res.name, ', '.join(match[0].name for match in
allMatches)))
See log for complete Python traceback.
> save "C:/Users/alex_/Downloads/Proyecto/Dianas limpias/8UFP.pdb"
> close
> open "C:/Users/alex_/Downloads/Proyecto/Dianas originales/5GNK.pdb"
5GNK.pdb title:
Crystal structure of EGFR 696-988 T790M In complex with LXX-6-34 [more
info...]
Chain information for 5GNK.pdb #1
---
Chain | Description | UniProt
A | epidermal growth factor receptor | EGFR_HUMAN 696-988
Non-standard residues in 5GNK.pdb #1
---
80U —
1-[(3R)-3-[4-azanyl-3-[3-chloranyl-4-[(1-methylimidazol-2-yl)methoxy]phenyl]pyrazolo[3,4-D]pyrimidin-1-yl]piperidin-1-yl]prop-2-en-1-one
CL — chloride ion
EDO — 1,2-ethanediol (ethylene glycol)
NO3 — nitrate ion
64 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> delete solvent
> delete ligand
> addh
Summary of feedback from adding hydrogens to 5GNK.pdb #1
---
warnings | Not adding hydrogens to /A GLU 697 CG because it is missing heavy-atom bond partners
Not adding hydrogens to /A GLU 736 CG because it is missing heavy-atom bond
partners
Not adding hydrogens to /A GLU 749 CG because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LYS 757 CG because it is missing heavy-atom bond
partners
Not adding hydrogens to /A GLN 976 CD (alt loc B) because it is missing heavy-
atom bond partners
1 messages similar to the above omitted
notes | Termini for 5GNK.pdb (#1) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A GLU 697, /A VAL 876
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A GLY 863, /A GLU 985
242 hydrogen bonds
Adding 'H' to /A GLU 697
Adding 'H' to /A VAL 876
/A GLU 985 is not terminus, removing H atom from 'C'
2264 hydrogens added
> addcharge
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue CL (net charge -1) with am1-bcc method
1 structure has non-integral total charge.
Details in log.
Here are the structures will non-integral total charge along with the
particular residues from those structures with non-integral total charge:
5GNK.pdb #1: /A GLU 697: -0.0828, /A GLU 736: -0.0828, /A GLU 749: -0.0828, /A
LYS 757: 0.0558, /A GLN 976: 0.6991, and /A GLU 985: -0.0618
> save "C:/Users/alex_/Downloads/Proyecto/Dianas limpias/5GNK.pdb"
> close
> open "C:/Users/alex_/Downloads/Proyecto/Dianas originales/5UG9.pdb"
5UG9.pdb title:
Crystal structure of the EGFR kinase domain (L858R, T790M, V948R) In complex
with A covalent inhibitor N-[(3R,4R)-4-fluoro-1-{6-[(3-
methoxy-1-methyl-1H-pyrazol-4-yl)amino]-9-(propan-2-yl)-9H-purin-2-
yl}pyrrolidin-3-yl]propanamide [more info...]
Chain information for 5UG9.pdb #1
---
Chain | Description | UniProt
A | epidermal growth factor receptor | EGFR_HUMAN 695-1022
Non-standard residues in 5UG9.pdb #1
---
8AM —
N-[(3R,4R)-4-fluoro-1-{6-[(3-methoxy-1-methyl-1H-pyrazol-4-yl)amino]-9-(propan-2-yl)-9H-purin-2-yl}pyrrolidin-3-yl]propanamide
EDO — 1,2-ethanediol (ethylene glycol)
GOL — glycerol (glycerin; propane-1,2,3-triol)
SO4 — sulfate ion
44 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> delete solvent
> delete ligand
> addh
Summary of feedback from adding hydrogens to 5UG9.pdb #1
---
notes | Termini for 5UG9.pdb (#1) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A ALA 702, /A PRO 753
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A ARG 748, /A GLU 985
258 hydrogen bonds
Adding 'H' to /A ALA 702
/A GLU 985 is not terminus, removing H atom from 'C'
2318 hydrogens added
> addcharge
Using Amber 20 recommended default charges and atom types for standard
residues
> MINIMIZE
Unknown command: MINIMIZE
> minimize
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Summary of feedback from adding hydrogens to 5UG9.pdb #1
---
notes | Termini for 5UG9.pdb (#1) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A ALA 702, /A PRO 753
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A ARG 748, /A GLU 985
252 hydrogen bonds
/A GLU 985 is not terminus, removing H atom from 'C'
0 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
Dock prep finished
> save "C:/Users/alex_/Downloads/Proyecto/Dianas limpias/5UG9.pdb"
> close
> open "C:\Users\alex_\Downloads\Proyecto\Dianas limpias\5GNK.pdb" format pdb
5GNK.pdb title:
Crystal structure of EGFR 696-988 T790M In complex with LXX-6-34 [more
info...]
Chain information for 5GNK.pdb #1
---
Chain | Description | UniProt
A | epidermal growth factor receptor | EGFR_HUMAN 696-988
Non-standard residues in 5GNK.pdb #1
---
CL — chloride ion
167 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> minimize
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Filling out missing side chains
/A GLU 697: phi none, psi -1.0 trans
/A GLU 736: phi -118.4, psi -1.2 trans
/A GLU 749: phi -64.0, psi 137.4 trans
/A LYS 757: phi -64.5, psi -39.3 trans
/A GLN 976: phi -68.0, psi -18.2 trans
/A GLU 985: phi -62.8, psi none trans
Applying GLU rotamer (chi angles: -66.2 82.2 1.9) to /A GLU 697
Applying GLU rotamer (chi angles: -63.3 -179.8 -3.7) to /A GLU 736
Applying GLU rotamer (chi angles: -64.9 86.2 -8.7) to /A GLU 749
Applying LYS rotamer (chi angles: -171.7 -89.7 -173.2 -177.4) to /A LYS 757
Applying GLN rotamer (chi angles: 69.0 -85.3 30.6) to /A GLN 976
Applying GLU rotamer (chi angles: -66.2 82.2 1.9) to /A GLU 985
Summary of feedback from adding hydrogens to 5GNK.pdb #1
---
notes | Termini for 5GNK.pdb (#1) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A GLU 697, /A VAL 876
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A GLY 863, /A GLU 985
242 hydrogen bonds
/A GLU 985 is not terminus, removing H atom from 'C'
33 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
Dock prep finished
> save "C:/Users/alex_/Downloads/Proyecto/Dianas limpias/5GNK.pdb"
> close
> open "C:/Users/alex_/Downloads/Proyecto/Dianas originales/7APF.pdb"
7APF.pdb title:
Crystal structure of JAK3 In complex with FM601 (compound 10A) [more info...]
Chain information for 7APF.pdb #1
---
Chain | Description | UniProt
A B | tyrosine-protein kinase JAK3 | JAK3_HUMAN 812-1103
Non-standard residues in 7APF.pdb #1
---
EDO — 1,2-ethanediol (ethylene glycol)
PHU — 1-phenylurea (phenylurea)
RQZ — 3-[3-(propanoylamino)phenyl]-1~{H}-pyrrolo[2,3-B]pyridine-5-carboxamide
86 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
4588 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> delete solvent
> delete ligand
> addh
Summary of feedback from adding hydrogens to 7APF.pdb #1
---
warnings | Not adding hydrogens to /A SER 1040 CB because it is missing heavy-atom bond partners
Not adding hydrogens to /B SER 897 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /B SER 1040 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /B ARG 1103 CB because it is missing heavy-atom bond
partners
notes | Termini for 7APF.pdb (#1) chain A determined from SEQRES records
Termini for 7APF.pdb (#1) chain B determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A PRO 814, /B PRO 814,
/B SER 897
Chain-final residues that are actual C termini: /A ARG 1103, /B ARG 1103
Chain-final residues that are not actual C termini: /B TYR 891
567 hydrogen bonds
Adding 'H' to /B SER 897
4544 hydrogens added
> addcharge
Using Amber 20 recommended default charges and atom types for standard
residues
1 structure has non-integral total charge.
Details in log.
Here are the structures will non-integral total charge along with the
particular residues from those structures with non-integral total charge:
7APF.pdb #1: /A SER 1040: 0.1567, /B SER 897: 0.1567, /B SER 1040: 0.1567, and
/B ARG 1103: -1.0687
> minimize
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Filling out missing side chains
/A SER 1040: phi -65.2, psi -34.1 trans
/B SER 897: phi none, psi -109.5 trans
/B SER 1040: phi -65.6, psi -32.9 trans
/B ARG 1103: phi 80.4, psi none trans
Applying SER rotamer (chi angles: 65.8) to /A SER 1040
Applying SER rotamer (chi angles: 65.3) to /B SER 897
Applying SER rotamer (chi angles: 65.8) to /B SER 1040
Applying ARG rotamer (chi angles: -171.0 -84.3 -176.8 -81.1) to /B ARG 1103
Summary of feedback from adding hydrogens to 7APF.pdb #1
---
notes | Termini for 7APF.pdb (#1) chain A determined from SEQRES records
Termini for 7APF.pdb (#1) chain B determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A PRO 814, /B PRO 814,
/B SER 897
Chain-final residues that are actual C termini: /A ARG 1103, /B ARG 1103
Chain-final residues that are not actual C termini: /B TYR 891
551 hydrogen bonds
20 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
Dock prep finished
> save "C:/Users/alex_/Downloads/Proyecto/Dianas limpias/7APF.pdb"
> close
> open "C:/Users/alex_/Downloads/Proyecto/Dianas originales/7C3N.pdb"
7C3N.pdb title:
Crystal structure of JAK3 In complex with delgocitinib [more info...]
Chain information for 7C3N.pdb #1
---
Chain | Description | UniProt
A | tyrosine-protein kinase JAK3 | JAK3_HUMAN 812-1124
Non-standard residues in 7C3N.pdb #1
---
FHX —
3-[(3S,4R)-3-methyl-7-(7H-pyrrolo[2,3-D]pyrimidin-4-yl)-1,7-diazaspiro[3.4]octan-1-yl]-3-oxidanylidene-
propanenitrile
107 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
2315 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> delete solvent
> delete ligand
> addh
Summary of feedback from adding hydrogens to 7C3N.pdb #1
---
notes | Termini for 7C3N.pdb (#1) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A PRO 814
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A SER 1102
290 hydrogen bonds
/A SER 1102 is not terminus, removing H atom from 'C'
2283 hydrogens added
> addcharge
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue PTR+PTR (net charge -4) with am1-bcc
method
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\TEMP~1.DES\AppData\Local\Temp\tmpbfyj4fxh\ante.in.mol2 -fi mol2 -o
C:\Users\TEMP~1.DES\AppData\Local\Temp\tmpbfyj4fxh\ante.out.mol2 -fo mol2 -c
bcc -nc -4 -j 5 -s 2 -dr n
(PTR+PTR) ``
(PTR+PTR) `Welcome to antechamber 20.0: molecular input file processor.`
(PTR+PTR) ``
(PTR+PTR) `Info: Finished reading file
(C:\Users\TEMP~1.DES\AppData\Local\Temp\tmpbfyj4fxh\ante.in.mol2); atoms read
(60), bonds read (61).`
(PTR+PTR) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(PTR+PTR) `Running: "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/bondtype" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(PTR+PTR) `bash.exe: warning: could not find /tmp, please create!`
(PTR+PTR) ``
(PTR+PTR) ``
(PTR+PTR) `Running: "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff`
(PTR+PTR) `bash.exe: warning: could not find /tmp, please create!`
(PTR+PTR) `Info: Total number of electrons: 292; net charge: -4`
(PTR+PTR) ``
(PTR+PTR) `Running: "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out`
(PTR+PTR) `bash.exe: warning: could not find /tmp, please create!`
(PTR+PTR) ``
(PTR+PTR) `Running: "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/am1bcc" -i ANTECHAMBER_AM1BCC_PRE.AC -o
ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`
(PTR+PTR) `bash.exe: warning: could not find /tmp, please create!`
(PTR+PTR) ``
(PTR+PTR) `Running: "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/atomtype" -f ac -p bcc -o
ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(PTR+PTR) `bash.exe: warning: could not find /tmp, please create!`
(PTR+PTR) ``
Charges for residue PTR+PTR determined
> minimize
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Summary of feedback from adding hydrogens to 7C3N.pdb #1
---
notes | Termini for 7C3N.pdb (#1) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A PRO 814
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A SER 1102
281 hydrogen bonds
/A SER 1102 is not terminus, removing H atom from 'C'
0 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue PTR+PTR (net charge -4) with am1-bcc
method
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\TEMP~1.DES\AppData\Local\Temp\tmp0qn9kqd7\ante.in.mol2 -fi mol2 -o
C:\Users\TEMP~1.DES\AppData\Local\Temp\tmp0qn9kqd7\ante.out.mol2 -fo mol2 -c
bcc -nc -4 -j 5 -s 2 -dr n
(PTR+PTR) ``
(PTR+PTR) `Welcome to antechamber 20.0: molecular input file processor.`
(PTR+PTR) ``
(PTR+PTR) `Info: Finished reading file
(C:\Users\TEMP~1.DES\AppData\Local\Temp\tmp0qn9kqd7\ante.in.mol2); atoms read
(60), bonds read (61).`
(PTR+PTR) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(PTR+PTR) `Running: "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/bondtype" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(PTR+PTR) `bash.exe: warning: could not find /tmp, please create!`
(PTR+PTR) ``
(PTR+PTR) ``
(PTR+PTR) `Running: "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff`
(PTR+PTR) `bash.exe: warning: could not find /tmp, please create!`
(PTR+PTR) `Info: Total number of electrons: 292; net charge: -4`
(PTR+PTR) ``
(PTR+PTR) `Running: "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out`
(PTR+PTR) `bash.exe: warning: could not find /tmp, please create!`
(PTR+PTR) ``
(PTR+PTR) `Running: "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/am1bcc" -i ANTECHAMBER_AM1BCC_PRE.AC -o
ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`
(PTR+PTR) `bash.exe: warning: could not find /tmp, please create!`
(PTR+PTR) ``
(PTR+PTR) `Running: "C:/Program Files/ChimeraX
1.11.dev202510140238/bin/amber20/bin/atomtype" -f ac -p bcc -o
ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(PTR+PTR) `bash.exe: warning: could not find /tmp, please create!`
(PTR+PTR) ``
Charges for residue PTR+PTR determined
Dock prep finished
> save "C:/Users/alex_/Downloads/Proyecto/Dianas limpias/7C3N.pdb"
> close
> open "C:/Users/alex_/Downloads/Proyecto/Dianas originales/6JQR.pdb"
6JQR.pdb title:
Crystal structure of FLT3 In complex with gilteritinib [more info...]
Chain information for 6JQR.pdb #1
---
Chain | Description | UniProt
A | receptor-type tyrosine-protein kinase FLT3,receptor-type tyrosine-protein kinase FLT3 | FLT3_HUMAN 571-710 762-951
Non-standard residues in 6JQR.pdb #1
---
C6F —
6-ethyl-3-[[3-methoxy-4-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]phenyl]amino]-5-(oxan-4-ylamino)pyrazine-2-carboxamide
(gilteritinib)
CXS — 3-cyclohexyl-1-propylsulfonic acid
GOL — glycerol (glycerin; propane-1,2,3-triol)
SO4 — sulfate ion
2361 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> delete solvent
> delete ligand
> addh
Summary of feedback from adding hydrogens to 6JQR.pdb #1
---
warnings | Not adding hydrogens to /A ARG 571 CB because it is missing heavy-atom bond partners
Not adding hydrogens to /A GLU 608 CG because it is missing heavy-atom bond
partners
Not adding hydrogens to /A GLU 611 CG because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LYS 614 CG because it is missing heavy-atom bond
partners
Not adding hydrogens to /A PHE 621 CB because it is missing heavy-atom bond
partners
18 messages similar to the above omitted
notes | Termini for 6JQR.pdb (#1) chain A determined from SEQRES records
Chain-initial residues that are actual N termini: /A ARG 571
Chain-initial residues that are not actual N termini: /A VAL 637, /A ASP 651,
/A ASN 781, /A MET 837
Chain-final residues that are actual C termini: /A GLU 951
Chain-final residues that are not actual C termini: /A SER 633, /A GLU 648, /A
SER 762, /A PHE 830
Missing OXT added to C-terminal residue /A GLU 951
289 hydrogen bonds
Adding 'H' to /A VAL 637
Adding 'H' to /A ASP 651
Adding 'H' to /A ASN 781
Adding 'H' to /A MET 837
2254 hydrogens added
> addcharge
Using Amber 20 recommended default charges and atom types for standard
residues
1 structure has non-integral total charge.
Details in log.
Here are the structures will non-integral total charge along with the
particular residues from those structures with non-integral total charge:
6JQR.pdb #1: /A ARG 571: 0.9892, /A GLU 608: -0.0828, /A GLU 611: -0.0828, /A
LYS 614: 0.0558, /A PHE 621: -0.0533, /A LYS 623: 0.0285, /A LYS 647: -0.0353,
/A GLU 648: -0.0618, /A ASP 651: -0.1722, /A SER 652: 0.1567, /A SER 653:
0.1567, /A ARG 655: 0.0675, /A GLU 708: -0.0828, /A LYS 709: 0.0558, /A ASN
781: -0.1994, /A LYS 797: 0.0285, /A LYS 823: 0.1384, /A MET 837: 0.0341, /A
SER 838: 0.1567, /A ASN 847: -0.1994, /A GLU 916: -0.0828, /A ILE 921: -0.037,
and /A PHE 942: -0.0533
> minimize
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Filling out missing side chains
/A ARG 571: phi none, psi 131.7 trans
/A GLU 608: phi -68.0, psi -15.7 trans
/A GLU 611: phi -109.1, psi 107.1 trans
/A LYS 614: phi -84.6, psi 160.8 trans
/A PHE 621: phi -83.1, psi -1.5 trans
/A LYS 623: phi -152.5, psi 158.0 trans
/A LYS 647: phi -75.0, psi 157.1 trans
/A GLU 648: phi -71.0, psi none trans
/A ASP 651: phi none, psi 171.0 trans
/A SER 652: phi -65.4, psi -30.8 trans
/A SER 653: phi -66.1, psi -36.4 trans
/A ARG 655: phi -52.4, psi -50.1 trans
/A GLU 708: phi -73.4, psi -31.6 trans
/A LYS 709: phi -97.4, psi 30.5 trans
/A ASN 781: phi none, psi -53.3 trans
/A LYS 797: phi -60.5, psi -45.8 trans
/A LYS 823: phi 49.1, psi 35.5 trans
/A MET 837: phi none, psi -58.7 trans
/A SER 838: phi -67.9, psi -24.7 trans
/A ASN 847: phi -73.2, psi -21.8 trans
/A GLU 916: phi -56.4, psi -37.9 trans
/A ILE 921: phi -63.1, psi -48.8 trans
/A PHE 942: phi -61.0, psi -43.9 trans
Applying ARG rotamer (chi angles: 178.1 66.9 -178.7 -85.3) to /A ARG 571
Applying GLU rotamer (chi angles: 66.6 -85.0 17.8) to /A GLU 608
Applying GLU rotamer (chi angles: -178.3 178.9 -1.7) to /A GLU 611
Applying LYS rotamer (chi angles: 67.3 -176.8 -70.4 -67.7) to /A LYS 614
Applying PHE rotamer (chi angles: -69.1 102.3) to /A PHE 621
Applying LYS rotamer (chi angles: -63.8 -178.0 -179.6 179.7) to /A LYS 623
Applying LYS rotamer (chi angles: -65.7 -178.5 176.7 65.8) to /A LYS 647
Applying GLU rotamer (chi angles: -66.2 82.2 1.9) to /A GLU 648
Applying ASP rotamer (chi angles: -72.1 -12.7) to /A ASP 651
Applying SER rotamer (chi angles: 65.8) to /A SER 652
Applying SER rotamer (chi angles: 64.6) to /A SER 653
Applying ARG rotamer (chi angles: -177.6 -174.5 63.4 79.8) to /A ARG 655
Applying GLU rotamer (chi angles: -65.3 82.2 1.8) to /A GLU 708
Applying LYS rotamer (chi angles: -64.6 -174.9 -71.5 -67.1) to /A LYS 709
Applying ASN rotamer (chi angles: -70.4 -23.2) to /A ASN 781
Applying LYS rotamer (chi angles: -174.7 178.4 -68.9 -68.5) to /A LYS 797
Applying LYS rotamer (chi angles: -61.1 -177.1 -178.7 178.6) to /A LYS 823
Applying MET rotamer (chi angles: -65.8 -61.8 -69.4) to /A MET 837
Applying SER rotamer (chi angles: 68.0) to /A SER 838
Applying ASN rotamer (chi angles: -169.0 174.6) to /A ASN 847
Applying GLU rotamer (chi angles: -67.0 81.2 -0.7) to /A GLU 916
Applying ILE rotamer (chi angles: -67.8 167.9) to /A ILE 921
Applying PHE rotamer (chi angles: -74.0 106.9) to /A PHE 942
Summary of feedback from adding hydrogens to 6JQR.pdb #1
---
notes | Termini for 6JQR.pdb (#1) chain A determined from SEQRES records
Chain-initial residues that are actual N termini: /A ARG 571
Chain-initial residues that are not actual N termini: /A VAL 637, /A ASP 651,
/A ASN 781, /A MET 837
Chain-final residues that are actual C termini: /A GLU 951
Chain-final residues that are not actual C termini: /A SER 633, /A GLU 648, /A
SER 762, /A PHE 830
289 hydrogen bonds
157 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
Dock prep finished
> save "C:/Users/alex_/Downloads/Proyecto/Dianas limpias/6JQR.pdb"
> close
> open "C:/Users/alex_/Downloads/Proyecto/Dianas originales/4XUF.pdb"
4XUF.pdb title:
Crystal structure of the FLT3 kinase domain bound to the inhibitor quizartinib
(AC220) [more info...]
Chain information for 4XUF.pdb #1
---
Chain | Description | UniProt
A B | receptor-type tyrosine-protein kinase FLT3 | FLT3_HUMAN 600-710 762-947
Non-standard residues in 4XUF.pdb #1
---
P30 — 1-(5-tert-
butyl-1,2-oxazol-3-yl)-3-(4-{7-[2-(morpholin-4-yl)ethoxy]imidazo[2,1-B][1,3]benzothiazol-2-yl}phenyl)urea
(quizartinib; PLX3397)
> delete solvent
> delete ligand
> addh
Summary of feedback from adding hydrogens to 4XUF.pdb #1
---
notes | Termini for 4XUF.pdb (#1) chain A determined from SEQRES records
Termini for 4XUF.pdb (#1) chain B determined from SEQRES records
Chain-initial residues that are actual N termini: /A ASP 600, /B ASP 600
Chain-initial residues that are not actual N termini: /A SER 652, /A LEU 783,
/B ASN 781
Chain-final residues that are actual C termini: /A LEU 947
Chain-final residues that are not actual C termini: /A GLU 648, /A ARG 707, /B
ARG 707, /B GLN 946
Missing OXT added to C-terminal residue /A LEU 947
429 hydrogen bonds
Adding 'H' to /A SER 652
Adding 'H' to /A LEU 783
Adding 'H' to /B ASN 781
/B GLN 946 is not terminus, removing H atom from 'C'
4330 hydrogens added
> addcharge
Using Amber 20 recommended default charges and atom types for standard
residues
> minimize
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Summary of feedback from adding hydrogens to 4XUF.pdb #1
---
notes | Termini for 4XUF.pdb (#1) chain A determined from SEQRES records
Termini for 4XUF.pdb (#1) chain B determined from SEQRES records
Chain-initial residues that are actual N termini: /A ASP 600, /B ASP 600
Chain-initial residues that are not actual N termini: /A SER 652, /A LEU 783,
/B ASN 781
Chain-final residues that are actual C termini: /A LEU 947
Chain-final residues that are not actual C termini: /A GLU 648, /A ARG 707, /B
ARG 707, /B GLN 946
410 hydrogen bonds
/B GLN 946 is not terminus, removing H atom from 'C'
0 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
Dock prep finished
> save "C:/Users/alex_/Downloads/Proyecto/Dianas limpias/4XUF.pdb"
> close
> open "C:/Users/alex_/Downloads/Proyecto/Dianas originales/5I4H.pdb"
5I4H.pdb title:
Caught In the act: the crystal structure of cleaved cathepsin L bound to the
active site of cathepsin L [more info...]
Chain information for 5I4H.pdb #1
---
Chain | Description | UniProt
A | cathepsin L1 | CATL1_HUMAN -1-105
B | cathepsin L1 | CATL1_HUMAN 109-220
Non-standard residues in 5I4H.pdb #1
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
SO4 — sulfate ion
67 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> delete solvent
> delete ligand
> addh
Summary of feedback from adding hydrogens to 5I4H.pdb #1
---
notes | Termini for 5I4H.pdb (#1) chain A determined from SEQRES records
Termini for 5I4H.pdb (#1) chain B determined from SEQRES records
Chain-initial residues that are actual N termini: /A GLU -1, /B ASP 109
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A SER 105, /B VAL 220
Chain-final residues that are not actual C termini:
169 hydrogen bonds
4 hydrogens added
> addcharge
Using Amber 20 recommended default charges and atom types for standard
residues
> minimize
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Summary of feedback from adding hydrogens to 5I4H.pdb #1
---
notes | Termini for 5I4H.pdb (#1) chain A determined from SEQRES records
Termini for 5I4H.pdb (#1) chain B determined from SEQRES records
Chain-initial residues that are actual N termini: /A GLU -1, /B ASP 109
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A SER 105, /B VAL 220
Chain-final residues that are not actual C termini:
169 hydrogen bonds
0 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.dev202510140238\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 322, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.11.dev202510140238\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.dev202510140238\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.dev202510140238\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.dev202510140238\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.dev202510140238\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 107, in prep
callback(session, state, structures)
File "C:\Program Files\ChimeraX 1.11.dev202510140238\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.dev202510140238\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.dev202510140238\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.dev202510140238\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.dev202510140238\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 156, in run_steps
callback()
File "C:\Program Files\ChimeraX 1.11.dev202510140238\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.dev202510140238\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.dev202510140238\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 174, in _minimize
system = forcefield.createSystem(top, nonbondedCutoff=1*nanometer,
constraints=HBonds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.dev202510140238\bin\Lib\site-
packages\openmm\app\forcefield.py", line 1280, in createSystem
raise Exception(msg)
Exception: Could not find typename 'N' for atom '<Atom 354 (N) of chain 0
residue 22 (A-CYS-22)>' 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.dev202510140238\bin\Lib\site-
packages\openmm\app\forcefield.py", line 1280, in createSystem
raise Exception(msg)
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 31.0.101.5333
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel
Python: 3.11.9
Locale: es_MX.cp1252
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: Vostro 3400
OS: Microsoft Windows 11 Pro (Build 26100)
Memory: 8,299,257,856
MaxProcessMemory: 137,438,953,344
CPU: 4 11th Gen Intel(R) Core(TM) i3-1115G4 @ 3.00GHz
OSLanguage: es-ES
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: 3.10.1
build: 1.3.0
certifi: 2025.10.5
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
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-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.17
ChimeraX-AtomicLibrary: 14.2.1
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.dev202510140238
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: 1.3.1
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: 0.2.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
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: 1.48.4
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.1
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: 7.10.7
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.17
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.60.1
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h5py: 3.15.0
html2text: 2025.4.15
idna: 3.11
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: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
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: 2.14.1
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: 4.5.0
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: 3.2.5
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: 2.32.5
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: 0.2.14
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
WMI: 1.5.1
Change History (3)
comment:1 by , 7 weeks ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Various minimize errors |
comment:3 by , 2 weeks ago
In 5i5h, residues 22 and 65 are disulphide bonded and yet also both have HG atoms.
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User deleted the heme but not the iron. This led to OpenMM raising an error since the singleton iron matches multiple templates. Since there is no way to tell ForceField how to disambiguate templates (only ForceField.createSystem() has provision for that), I'm stuck. Have complained on the OpenMM GitHub