Possible MD template error

[arotsch@…]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Failed to add atoms ['H23'] to atom N2 because this will lead to having 4 atoms attached, which is more than its assigned geometry can support. This is probably due to an error in the MD template (MC_MGT).

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/arotsch/Documents/combination_lastframe_7qtl_7kl3-coot-3_2.pdb

Summary of feedback from opening
/Users/arotsch/Documents/combination_lastframe_7qtl_7kl3-coot-3_2.pdb  
---  
warnings | Cannot find LINK/SSBOND residue RQA (101 )  
PDB SEQRES record for chain G is incomplete. Ignoring input sequence records
as basis for sequence.  
  
Chain information for combination_lastframe_7qtl_7kl3-coot-3_2.pdb #1  
---  
Chain | Description  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
G | No description available  
R | No description available  
V | No description available  
X | No description available  
Y | No description available  
  

> open /Users/arotsch/Downloads/cryosparc_P202_J378_005_volume_map_sharp.mrc

Opened cryosparc_P202_J378_005_volume_map_sharp.mrc as #2, grid size
448,448,448, pixel 1.05, shown at level 0.263, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.6363

> hide atoms

> show cartoons

> style stick

Changed 18221 atom styles  

> show atoms

> isolde start

> set selectionWidth 4

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 191 residues in model #1 to IUPAC-IUB
standards.  
Chain information for combination_lastframe_7qtl_7kl3-coot-3_2.pdb  
---  
Chain | Description  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
1.2/E | No description available  
1.2/G | No description available  
1.2/R | No description available  
1.2/V | No description available  
1.2/X | No description available  
1.2/Y | No description available  
  

> clipper associate #2 toModel #1

Opened cryosparc_P202_J378_005_volume_map_sharp.mrc as #1.1.1.1, grid size
448,448,448, pixel 1.05, shown at step 1, values float32  

> isolde sim start /B,R-Y,G,D-E,C

Loading residue template for MGT from internal database  
Sim termination reason: None  
ISOLDE: stopped sim  

> addh #1.2

Summary of feedback from adding hydrogens to
combination_lastframe_7qtl_7kl3-coot-3_2.pdb #1.2  
---  
warnings | Not adding hydrogens to /B A 1 P because it is missing heavy-atom
bond partners  
Not adding hydrogens to /R C 6 P because it is missing heavy-atom bond
partners  
Not adding hydrogens to /R U 13 P because it is missing heavy-atom bond
partners  
Not adding hydrogens to /Y PRO 13 N because it is missing heavy-atom bond
partners  
Not adding hydrogens to /Y PRO 13 CB because it is missing heavy-atom bond
partners  
1 messages similar to the above omitted  
Unknown hybridization for atom (PG) of residue type MGT; not adding hydrogens
to it  
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /Y PRO 13 N  
notes | Termini for combination_lastframe_7qtl_7kl3-coot-3_2.pdb (#1.2) chain
B determined from SEQRES records  
No usable SEQRES records for combination_lastframe_7qtl_7kl3-coot-3_2.pdb
(#1.2) chain C; guessing termini instead  
No usable SEQRES records for combination_lastframe_7qtl_7kl3-coot-3_2.pdb
(#1.2) chain D; guessing termini instead  
No usable SEQRES records for combination_lastframe_7qtl_7kl3-coot-3_2.pdb
(#1.2) chain E; guessing termini instead  
No usable SEQRES records for combination_lastframe_7qtl_7kl3-coot-3_2.pdb
(#1.2) chain G; guessing termini instead  
Termini for combination_lastframe_7qtl_7kl3-coot-3_2.pdb (#1.2) chain R
determined from SEQRES records  
Termini for combination_lastframe_7qtl_7kl3-coot-3_2.pdb (#1.2) chain V
determined from SEQRES records  
Termini for combination_lastframe_7qtl_7kl3-coot-3_2.pdb (#1.2) chain X
determined from SEQRES records  
Termini for combination_lastframe_7qtl_7kl3-coot-3_2.pdb (#1.2) chain Y
determined from SEQRES records  
Chain-initial residues that are actual N termini: /C MET 1, /D GLY 0, /E MET
1, /X TYR 1, /D GLY 0, /D LEU 72, /E MET 1, /E LYS 207, /E ASN 676, /C MET 1,
/C GLU 492  
Chain-initial residues that are not actual N termini: /C GLU 492, /D LEU 72,
/E LYS 207, /E ASN 676, /Y PRO 13  
Chain-final residues that are actual C termini: /C ARG 737, /D ARG 716, /E LYS
757, /D ILE 63, /D ARG 716, /E HIS 184, /E SER 673, /E LYS 757, /C MET 483, /C
ARG 737  
Chain-final residues that are not actual C termini: /C MET 483, /D ILE 63, /E
HIS 184, /E SER 673, /X PRO 6, /Y TYR 22  
Chain-initial residues that are not actual 5' termini: /R C 6  
1559 hydrogen bonds  
Adding 'H' to /C GLU 492  
Adding 'H' to /D LEU 72  
Adding 'H' to /E LYS 207  
Adding 'H' to /E ASN 676  
/X PRO 6 is not terminus, removing H atom from 'C'  
/Y TYR 22 is not terminus, removing H atom from 'C'  
/B G 2 is not terminus, removing H atom from O3'  
/V G 15 is not terminus, removing H atom from O3'  
17893 hydrogens added  
  
Fetching CCD PCA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/PCA/PCA.cif  
Fetching CCD HY3 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/3/HY3/HY3.cif  
Fetching CCD AYA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/AYA/AYA.cif  
Fetching CCD CSO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/CSO/CSO.cif  
Fetching CCD ORN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ORN/ORN.cif  
Fetching CCD CSS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/CSS/CSS.cif  
Deleted the following atoms from residue A V1: OP1  
Residue U R13 has only 2 atoms in common with the template. At least 3 are
needed to rebuild automatically. Adding of nucleic acid residues is not
currently possible in ISOLDE. To move forward, just delete this residue.  
[Repeated 1 time(s)]Deleted the following atoms from residue MGT G1: H1G,
H5'', H8, H1, H2G, H21, H5', H22  
Failed to add atoms ['H23'] to atom N2 because this will lead to having 4
atoms attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (MC_MGT). If this template is
built into ISOLDE, please report this using Help/Report a bug  

MD template PRO for residue PRO Y13 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

> delete sel

Fetching CCD N7P from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/N7P/N7P.cif  
Fetching CCD FME from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/FME/FME.cif  

MD template PRO for residue PRO Y13 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

The atom CG in MD template PRO bonds to more than one existing atom in residue
PRO. Since MD templates do not explicitly specify geometry, this type of atom
addition is not currently supported. The resulting residue will contain only
those atoms which the MD and coordinate templates have in common  

> delete sel

Failed to add atoms ['H23'] to atom N2 because this will lead to having 4
atoms attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (MC_MGT). If this template is
built into ISOLDE, please report this using Help/Report a bug  

> isolde sim start /G:1

Sim termination reason: None  
ISOLDE: stopped sim  
Failed to add atoms ['H23'] to atom N2 because this will lead to having 4
atoms attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (MC_MGT). If this template is
built into ISOLDE, please report this using Help/Report a bug  

> ui mousemode right select

> select /G:1@N2

1 atom, 1 residue, 1 model selected  

> select /G:1@N2

1 atom, 1 residue, 1 model selected  

> select /G:1@N2

1 atom, 1 residue, 1 model selected  

> select clear

> select /G:1@N3

1 atom, 1 residue, 1 model selected  

> select /G:1@N3

1 atom, 1 residue, 1 model selected  
Failed to add atoms ['H23'] to atom N2 because this will lead to having 4
atoms attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (MC_MGT). If this template is
built into ISOLDE, please report this using Help/Report a bug  
[Repeated 7 time(s)]




OpenGL version: 4.1 ATI-3.10.23
OpenGL renderer: AMD Radeon Pro 580X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac19,1
      Processor Name: 6-Core Intel Core i5
      Processor Speed: 3,7 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 9 MB
      Memory: 32 GB
      Boot ROM Version: 1731.140.1.0.0
      SMC Version (system): 2.46f13

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H2026)
      Kernel Version: Darwin 19.6.0
      Time since boot: 4 days 21:57

Graphics/Displays:

    Radeon Pro 580X:

      Chipset Model: Radeon Pro 580X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D0008A-042
      VBIOS Version: 113-D0008A1X-009
      EFI Driver Version: 01.B1.042
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: 5120 x 2880 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
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[Eric Pettersen]

Reported by Alexander Rotsch

[Tristan Croll]

Corrected parameterisation of ligand MGD

[Tristan Croll]

Thanks for reporting this! The automated script (developed by Nigel Moriarty and David Case) used to generate the set of templates bundled with ISOLDE had a tendency to mistakenly assign certain nitrogens as primary amines - in your case, the -NH2 groups of the guanidinium-like rings. If you run into others please continue to report them, but in the meantime you can work around the issue as follows:

• make sure your ligand is complete with all the hydrogens in the right places.
• select at least one atom from the ligand, and use the command "isolde param sel override t"
• if ISOLDE is already running you should be free to continue. The command will write a {residue name}.xml file to the current working directory. For future ISOLDE sessions, use the "Load residue parameters" button in the Residue Parameterisation widget to add this file to the working force field.

I've attached a parameterisation file for your ligand, which should get you going for the time being. Once I'm back from holiday I'll replace the entry in ISOLDE's template library.