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Opened 3 weeks ago
Last modified 3 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 (1)
comment:1 by , 3 weeks ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Various minimize errors |
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