Antechamber doesn't like blank residue name

[Tristan Croll]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.7.dev202307112022 (2023-07-11 20:22:49 UTC)
Description
Problem originally arose in the "isolde paramerterize" command, but it also affects AddCharge so reporting it here. The residue in the attached file has a residue name of "0", which somehow breaks Antechamber. From a little googling, the warnings that arise ("the best APS is not zero") are usually caused by unrecognised elements, so I'm not sure what's going on here. Anyway, this causes "isolde param" to crash and burn entirely. AddCharge goes through, but the charges are wrong. Simply renaming the residue seems to get things working correctly.

Charges with the residue as-loaded:
array([ 0.021   , -0.099   , -0.099   ,  0.021   , -0.099   , -0.099   ,
       -0.099   , -0.099   , -0.099   , -0.099   ,  0.194222,  0.194222,
        0.194222,  0.194222,  0.194222,  0.194222,  0.194222,  0.194222,
        0.194222])

Charges after renaming the residue to PGN:
array([-0.8526,  0.2949,  0.1217, -0.2038, -0.2063, -0.092 , -0.1155,
       -0.064 , -0.1155, -0.092 ,  0.1387,  0.144 ,  0.167 ,  0.168 ,
        0.167 ,  0.144 ,  0.4648,  0.4648,  0.4648])

Log:
> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.7.dev202307112022 (2023-07-11)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/Tristan Croll/Downloads/PGN_R.pdb"

PGN_R.pdb title:  
PGN_R [more info...]  
  
Non-standard residues in PGN_R.pdb #1  
---  
— ()  
  

> coulombic #1

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue (net charge +1) with am1-bcc method  
Running ANTECHAMBER command: C:/Program Files/ChimeraX-
daily/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\TRISTA~1\AppData\Local\Temp\tmprxxx47_o\ante.in.mol2 -fi mol2 -o
C:\Users\TRISTA~1\AppData\Local\Temp\tmprxxx47_o\ante.out.mol2 -fo mol2 -c bcc
-nc 1 -j 5 -s 2 -dr n  
() ``  
() `Welcome to antechamber 20.0: molecular input file processor.`  
() ``  
() `Info: Finished reading file
(C:\Users\TRISTA~1\AppData\Local\Temp\tmprxxx47_o\ante.in.mol2); atoms read
(19), bonds read (0).`  
() `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
() ``  
() `Running: "C:/Program Files/ChimeraX-daily/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
() `bash.exe: warning: could not find /tmp, please create!`  
() `Info: Total number of electrons: 70; net charge: 1`  
() ``  
() `Running: "C:/Program Files/ChimeraX-daily/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`  
() `bash.exe: warning: could not find /tmp, please create!`  
() ``  
() `Running: "C:/Program Files/ChimeraX-daily/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX-daily/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 5`  
() `bash.exe: warning: could not find /tmp, please create!`  
() ``  
() `Running: "C:/Program Files/ChimeraX-daily/bin/amber20/bin/bondtype" -f ac
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
() `bash.exe: warning: could not find /tmp, please create!`  
() `Warning: For atom (ID: 1, Name: N1) the best APS is not zero.`  
() ` Bonds involving this atom are frozen.`  
() `Warning: For atom (ID: 4, Name: N2) the best APS is not zero.`  
() ` Bonds involving this atom are frozen.`  
() ``  
() ``  
() `Running: "C:/Program Files/ChimeraX-daily/bin/amber20/bin/atomtype" -f ac
-p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC.AC`  
() `bash.exe: warning: could not find /tmp, please create!`  
() ``  
Charges for residue determined  
Coulombic values for PGN_R.pdb_ SES surface #1.1: minimum, 1.56, mean 4.78,
maximum 8.66  

> usage coul

coulombic [atoms] [surfaces a surfaces specifier] [gpadding a number] [map
true or false] [gspacing a number] [hisScheme hisScheme] [offset a number]
[palette a colormap] [range range] [distDep true or false] [dielectric a
number] [chargeMethod chargeMethod] [key true or false]  
— Color surfaces by coulombic potential  
atoms: an atoms specifier or nothing  
hisScheme: one of HID, HIE, or HIP  
range: some numbers or full  
chargeMethod: one of am1-bcc or gasteiger  

> close

> open "C:\Users\Tristan Croll\Downloads\PGN_R.pdb" format pdb

PGN_R.pdb title:  
PGN_R [more info...]  
  
Non-standard residues in PGN_R.pdb #1  
---  
— ()  
  

> setattr #1 res name PGN

Assigning name attribute to 1 item  

> coulombic #1

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue PGN (net charge +1) with am1-bcc method  
Running ANTECHAMBER command: C:/Program Files/ChimeraX-
daily/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\TRISTA~1\AppData\Local\Temp\tmpmn1wdd9q\ante.in.mol2 -fi mol2 -o
C:\Users\TRISTA~1\AppData\Local\Temp\tmpmn1wdd9q\ante.out.mol2 -fo mol2 -c bcc
-nc 1 -j 5 -s 2 -dr n  
(PGN) ``  
(PGN) `Welcome to antechamber 20.0: molecular input file processor.`  
(PGN) ``  
(PGN) `Info: Finished reading file
(C:\Users\TRISTA~1\AppData\Local\Temp\tmpmn1wdd9q\ante.in.mol2); atoms read
(19), bonds read (19).`  
(PGN) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(PGN) `Running: "C:/Program Files/ChimeraX-daily/bin/amber20/bin/bondtype" -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(PGN) `bash.exe: warning: could not find /tmp, please create!`  
(PGN) ``  
(PGN) ``  
(PGN) `Running: "C:/Program Files/ChimeraX-daily/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(PGN) `bash.exe: warning: could not find /tmp, please create!`  
(PGN) `Info: Total number of electrons: 70; net charge: 1`  
(PGN) ``  
(PGN) `Running: "C:/Program Files/ChimeraX-daily/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`  
(PGN) `bash.exe: warning: could not find /tmp, please create!`  
(PGN) ``  
(PGN) `Running: "C:/Program Files/ChimeraX-daily/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX-daily/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
(PGN) `bash.exe: warning: could not find /tmp, please create!`  
(PGN) ``  
(PGN) `Running: "C:/Program Files/ChimeraX-daily/bin/amber20/bin/atomtype" -f
ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(PGN) `bash.exe: warning: could not find /tmp, please create!`  
(PGN) ``  
Charges for residue PGN determined  
Coulombic values for PGN_R.pdb_ SES surface #1.1: minimum, 0.78, mean 4.95,
maximum 9.45  

> open "C:/Users/Tristan Croll/Downloads/PGN_R.pdb"

PGN_R.pdb title:  
PGN_R [more info...]  
  
Non-standard residues in PGN_R.pdb #2  
---  
— ()  
  

> select #2

19 atoms, 19 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected atoms"

> coulombic #2

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue (net charge +1) with am1-bcc method  
Running ANTECHAMBER command: C:/Program Files/ChimeraX-
daily/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\TRISTA~1\AppData\Local\Temp\tmpnha6mk75\ante.in.mol2 -fi mol2 -o
C:\Users\TRISTA~1\AppData\Local\Temp\tmpnha6mk75\ante.out.mol2 -fo mol2 -c bcc
-nc 1 -j 5 -s 2 -dr n  
() ``  
() `Welcome to antechamber 20.0: molecular input file processor.`  
() ``  
() `Info: Finished reading file
(C:\Users\TRISTA~1\AppData\Local\Temp\tmpnha6mk75\ante.in.mol2); atoms read
(19), bonds read (0).`  
() `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
() ``  
() `Running: "C:/Program Files/ChimeraX-daily/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
() `bash.exe: warning: could not find /tmp, please create!`  
() `Info: Total number of electrons: 70; net charge: 1`  
() ``  
() `Running: "C:/Program Files/ChimeraX-daily/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`  
() `bash.exe: warning: could not find /tmp, please create!`  
() ``  
() `Running: "C:/Program Files/ChimeraX-daily/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX-daily/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 5`  
() `bash.exe: warning: could not find /tmp, please create!`  
() ``  
() `Running: "C:/Program Files/ChimeraX-daily/bin/amber20/bin/bondtype" -f ac
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
() `bash.exe: warning: could not find /tmp, please create!`  
() `Warning: For atom (ID: 1, Name: N1) the best APS is not zero.`  
() ` Bonds involving this atom are frozen.`  
() `Warning: For atom (ID: 4, Name: N2) the best APS is not zero.`  
() ` Bonds involving this atom are frozen.`  
() ``  
() ``  
() `Running: "C:/Program Files/ChimeraX-daily/bin/amber20/bin/atomtype" -f ac
-p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC.AC`  
() `bash.exe: warning: could not find /tmp, please create!`  
() ``  
Charges for residue determined  
Coulombic values for PGN_R.pdb_ SES surface #2.1: minimum, 1.56, mean 4.78,
maximum 8.66  

> ui tool show Shell

0.01s - Debugger warning: It seems that frozen modules are being used, which
may  
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off  
0.00s - to python to disable frozen modules.  
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to
disable this validation.  




OpenGL version: 3.3.0 NVIDIA 518.01
OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_GB.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

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Model: HP ZBook Studio 15.6 inch G8 Mobile Workstation PC
OS: Microsoft Windows 11 Pro (Build 22621)
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MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz
OSLanguage: en-GB

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    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.2
    traitlets: 5.9.0
    typing-extensions: 4.7.1
    tzdata: 2023.3
    urllib3: 2.0.3
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.8
    WMI: 1.5.1
File attachment: PGN_R.pdb

PGN_R.pdb​

[Tristan Croll]

Added by email2trac

[Eric Pettersen]

The residue name isn't "0" -- the residue name is blank. The residue number is 0. I have added code to add_charge to guard against sending blank residue names to Antechamber.

Fix: ​https://github.com/RBVI/ChimeraX/commit/7e895f509e5028d30a56f111be63da6ba56ab98d