Coulombic coloring fails on 7mjo, sqm cannot handle HIS+HIS

[philip.macmenamin@…]

The following bug report has been submitted:
Platform:        macOS-11.6-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202110062055 (2021-10-06 20:55:38 UTC)
Description
Philip MacMenamin reported coulomb surface coloring failing for the NIH 3D pipeline on 7mjo with a Amber failure computing charges for ligand HIS+HIS.   It also fails for me (after 16 minutes) with sqm giving up.

Log:
UCSF ChimeraX version: 1.3.dev202110062055 (2021-10-06)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7mjo

Summary of feedback from opening 7mjo fetched from pdb  
---  
warnings | Unable to fetch template for 'K': might have incorrect bonds  
Unable to fetch template for 'ATP': might have incorrect bonds  
Unable to fetch template for 'PTY': might have incorrect bonds  
notes | Fetching compressed mmCIF 7mjo from
http://files.rcsb.org/download/7mjo.cif  
Fetching CCD POV from http://ligand-expo.rcsb.org/reports/P/POV/POV.cif  
Fetching CCD GBM from http://ligand-expo.rcsb.org/reports/G/GBM/GBM.cif  
  
7mjo title:  
Vascular KATP channel: Kir6.1 SUR2B quatrefoil-like conformation 1 [more
info...]  
  
Chain information for 7mjo #1  
---  
Chain | Description | UniProt  
A B C D | ATP-sensitive inward rectifier potassium channel 8 | KCNJ8_RAT  
E G | Isoform SUR2B of ATP-binding cassette sub-family C member 9 | ABCC9_RAT  
  
Non-standard residues in 7mjo #1  
---  
ATP — adenosine-5'-triphosphate  
GBM —
5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide
(Glibenclamide; Glyburide)  
K — potassium ion  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
POV — (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl
2-(trimethylammonio)ethyl phosphate (POPC)  
PTY — phosphatidylethanolamine  
  

> coulombic

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/A LYS 24  
/A ARG 26  
/A ILE 27  
/A ARG 28  
/A ASP 29  
/A ARG 30  
/A LEU 31  
/A SER 40  
/A LYS 48  
/A GLU 52  
/A GLN 53  
/A GLN 58  
/A LYS 68  
/A ARG 70  
/A LEU 85  
/A ILE 89  
/A ASP 100  
/A GLU 106  
/A LYS 107  
/A ILE 109  
/A THR 110  
/A GLU 111  
/A LYS 112  
/A SER 113  
/A LEU 115  
/A GLU 116  
/A SER 117  
/A VAL 119  
/A THR 122  
/A SER 134  
/A GLU 136  
/A MET 148  
/A THR 149  
/A GLU 150  
/A GLU 151  
/A THR 157  
/A VAL 172  
/A MET 173  
/A ILE 177  
/A LYS 180  
/A GLN 183  
/A ARG 187  
/A GLU 189  
/A SER 194  
/A VAL 198  
/A PHE 210  
/A ILE 227  
/A GLU 237  
/A GLU 239  
/A VAL 241  
/A ILE 248  
/A VAL 250  
/A VAL 262  
/A ILE 266  
/A ILE 267  
/A CYS 268  
/A VAL 270  
/A ILE 271  
/A ASP 272  
/A LYS 273  
/A ILE 280  
/A SER 281  
/A GLN 288  
/A ASP 289  
/A LEU 290  
/A ILE 295  
/A THR 306  
/A THR 311  
/A SER 312  
/A ILE 314  
/A GLU 317  
/A GLU 331  
/A GLU 332  
/A SER 336  
/A VAL 348  
/A CYS 353  
/A SER 354  
/A ARG 356  
/A GLU 357  
/A LEU 358  
/A ASP 359  
/A GLU 360  
/A LYS 361  
/A SER 363  
/A ILE 364  
/A LEU 365  
/A ILE 366  
/A GLN 367  
/A THR 368  
/B ARG 30  
/B LEU 31  
/B LYS 33  
/B LEU 45  
/B ILE 50  
/B ASP 66  
/B ILE 75  
/B LEU 81  
/B ILE 89  
/B ASP 100  
/B ILE 101  
/B GLU 106  
/B LYS 107  
/B ILE 109  
/B THR 110  
/B GLU 111  
/B LYS 112  
/B SER 113  
/B LEU 115  
/B GLU 116  
/B SER 117  
/B VAL 139  
/B ILE 141  
/B GLU 150  
/B GLN 162  
/B ILE 169  
/B THR 181  
/B GLN 183  
/B GLU 189  
/B THR 190  
/B ILE 192  
/B VAL 198  
/B ARG 211  
/B VAL 212  
/B LYS 217  
/B SER 218  
/B MET 219  
/B ILE 220  
/B ILE 221  
/B SER 224  
/B VAL 225  
/B VAL 230  
/B ILE 248  
/B VAL 250  
/B ASP 251  
/B SER 256  
/B ASN 257  
/B ASN 258  
/B LEU 265  
/B ILE 266  
/B ILE 267  
/B CYS 268  
/B VAL 270  
/B LYS 273  
/B SER 275  
/B THR 283  
/B ASP 284  
/B VAL 286  
/B ILE 295  
/B GLU 297  
/B THR 302  
/B THR 303  
/B THR 311  
/B ILE 314  
/B HIS 322  
/B VAL 325  
/B SER 326  
/B GLU 330  
/B GLU 332  
/B ARG 356  
/B GLU 357  
/B ASP 359  
/B GLU 360  
/B LYS 361  
/B SER 363  
/B ILE 364  
/B LEU 365  
/B ILE 366  
/C LEU 31  
/C ARG 35  
/C ILE 50  
/C GLU 52  
/C GLN 53  
/C ARG 55  
/C ASP 66  
/C ILE 75  
/C ILE 89  
/C ASP 100  
/C MET 105  
/C GLU 106  
/C LYS 107  
/C ILE 109  
/C THR 110  
/C GLU 111  
/C LYS 112  
/C SER 113  
/C LEU 115  
/C GLU 116  
/C SER 117  
/C VAL 119  
/C ARG 125  
/C THR 128  
/C LEU 132  
/C ILE 135  
/C GLU 136  
/C GLU 150  
/C ILE 164  
/C ILE 169  
/C ILE 177  
/C GLU 189  
/C THR 190  
/C VAL 198  
/C LYS 205  
/C PHE 208  
/C ASP 214  
/C LYS 217  
/C MET 219  
/C ILE 221  
/C SER 222  
/C GLU 239  
/C ILE 248  
/C GLU 255  
/C LEU 261  
/C LEU 265  
/C CYS 268  
/C HIS 269  
/C ASP 272  
/C LYS 273  
/C ASP 279  
/C ASP 284  
/C VAL 292  
/C VAL 299  
/C GLU 301  
/C SER 312  
/C ILE 314  
/C GLU 316  
/C GLU 317  
/C SER 326  
/C THR 329  
/C GLU 330  
/C GLU 331  
/C GLU 332  
/C SER 340  
/C ARG 356  
/C GLU 357  
/C LEU 358  
/C ASP 359  
/C GLU 360  
/C LYS 361  
/C SER 363  
/C ILE 364  
/C LEU 365  
/C ILE 366  
/C GLN 367  
/D ARG 30  
/D LEU 31  
/D GLU 52  
/D ARG 55  
/D GLN 58  
/D ASP 59  
/D VAL 94  
/D ASP 100  
/D ILE 101  
/D MET 105  
/D GLU 106  
/D LYS 107  
/D ILE 109  
/D THR 110  
/D GLU 111  
/D LYS 112  
/D SER 113  
/D LEU 115  
/D GLU 116  
/D SER 117  
/D SER 126  
/D SER 129  
/D GLU 136  
/D VAL 137  
/D GLN 162  
/D ILE 168  
/D ILE 169  
/D ILE 177  
/D THR 181  
/D HIS 185  
/D GLU 189  
/D ILE 199  
/D CYS 207  
/D VAL 212  
/D LYS 217  
/D MET 219  
/D ILE 220  
/D GLU 239  
/D VAL 241  
/D VAL 262  
/D LEU 265  
/D ILE 267  
/D CYS 268  
/D HIS 269  
/D LYS 273  
/D ARG 274  
/D LEU 277  
/D ASP 279  
/D ILE 280  
/D SER 281  
/D LEU 285  
/D VAL 286  
/D ASN 287  
/D VAL 294  
/D THR 303  
/D THR 306  
/D ILE 314  
/D GLU 316  
/D VAL 328  
/D GLU 330  
/D GLU 331  
/D GLU 332  
/D VAL 337  
/D SER 340  
/D ASN 344  
/D VAL 348  
/D ARG 356  
/D GLU 357  
/D LEU 358  
/D ASP 359  
/D GLU 360  
/D LYS 361  
/D SER 363  
/D ILE 364  
/D LEU 365  
/D ILE 366  
/E SER 2  
/E LEU 3  
/E SER 4  
/E ILE 10  
/E SER 11  
/E SER 12  
/E ASN 14  
/E ILE 15  
/E ASP 27  
/E LEU 29  
/E ASN 30  
/E VAL 35  
/E PHE 36  
/E LEU 37  
/E ILE 40  
/E LEU 45  
/E SER 51  
/E GLN 52  
/E SER 53  
/E SER 54  
/E LYS 55  
/E VAL 56  
/E GLN 57  
/E ILE 58  
/E HIS 59  
/E HIS 60  
/E ASN 61  
/E THR 62  
/E TRP 63  
/E LEU 64  
/E HIS 65  
/E PHE 66  
/E ASN 70  
/E ARG 72  
/E ILE 74  
/E LEU 75  
/E PHE 77  
/E LEU 79  
/E LEU 80  
/E VAL 84  
/E CYS 85  
/E GLU 86  
/E ILE 87  
/E GLU 89  
/E SER 93  
/E ASP 94  
/E SER 95  
/E SER 99  
/E LEU 102  
/E LEU 104  
/E MET 106  
/E THR 117  
/E SER 118  
/E GLU 126  
/E THR 127  
/E SER 128  
/E ASN 129  
/E LEU 133  
/E LEU 135  
/E ILE 146  
/E THR 147  
/E LYS 154  
/E LEU 158  
/E MET 162  
/E SER 163  
/E ASP 164  
/E LEU 165  
/E PHE 167  
/E CYS 168  
/E ILE 169  
/E ILE 175  
/E LEU 176  
/E ASN 177  
/E LEU 179  
/E MET 181  
/E VAL 183  
/E GLU 184  
/E ILE 185  
/E ASN 186  
/E VAL 187  
/E ILE 188  
/E ARG 191  
/E ARG 192  
/E TYR 193  
/E VAL 194  
/E PHE 195  
/E PHE 196  
/E MET 197  
/E VAL 213  
/E ARG 214  
/E PHE 215  
/E LEU 216  
/E GLN 217  
/E PHE 219  
/E VAL 220  
/E ASN 221  
/E LEU 222  
/E LEU 223  
/E SER 224  
/E LYS 225  
/E MET 231  
/E ASN 232  
/E THR 233  
/E LEU 234  
/E ILE 235  
/E ILE 236  
/E SER 237  
/E HIS 239  
/E ARG 240  
/E LYS 241  
/E ILE 243  
/E ASP 244  
/E LEU 245  
/E LYS 246  
/E ILE 248  
/E LYS 250  
/E LEU 251  
/E ILE 253  
/E MET 255  
/E ARG 256  
/E VAL 258  
/E THR 259  
/E ASN 260  
/E TYR 261  
/E VAL 262  
/E CYS 263  
/E LYS 265  
/E GLU 266  
/E TYR 268  
/E GLU 269  
/E GLU 270  
/E GLN 271  
/E LYS 272  
/E LYS 273  
/E LYS 274  
/E ASP 277  
/E HIS 278  
/E ASN 280  
/E ARG 281  
/E THR 282  
/E PRO 283  
/E SER 284  
/E ILE 285  
/E TRP 286  
/E LEU 287  
/E MET 289  
/E ARG 291  
/E ARG 295  
/E ILE 297  
/E LEU 298  
/E LEU 299  
/E SER 300  
/E SER 301  
/E THR 302  
/E LEU 306  
/E ASP 308  
/E LEU 309  
/E LEU 310  
/E PHE 312  
/E LEU 316  
/E CYS 317  
/E ILE 318  
/E ILE 321  
/E ARG 324  
/E VAL 325  
/E ASN 326  
/E GLU 327  
/E LYS 329  
/E ASN 330  
/E ASN 331  
/E THR 332  
/E THR 333  
/E ARG 334  
/E PHE 335  
/E SER 336  
/E GLU 337  
/E LEU 339  
/E SER 341  
/E LYS 342  
/E GLU 343  
/E LEU 345  
/E HIS 349  
/E LEU 351  
/E ILE 360  
/E GLN 362  
/E ARG 363  
/E PHE 365  
/E LEU 366  
/E GLN 367  
/E SER 369  
/E TYR 371  
/E VAL 372  
/E THR 373  
/E ILE 374  
/E GLU 375  
/E THR 376  
/E ILE 378  
/E ASN 379  
/E LEU 380  
/E ARG 381  
/E LEU 384  
/E LEU 385  
/E ILE 388  
/E TYR 389  
/E LYS 391  
/E ILE 392  
/E LEU 393  
/E ARG 394  
/E LEU 395  
/E SER 396  
/E THR 397  
/E SER 398  
/E ASN 399  
/E LEU 400  
/E SER 401  
/E MET 402  
/E GLU 404  
/E MET 405  
/E THR 406  
/E LEU 407  
/E GLN 409  
/E ILE 410  
/E ASN 411  
/E ASN 412  
/E LEU 413  
/E VAL 414  
/E ILE 416  
/E GLU 417  
/E ASN 419  
/E GLN 420  
/E PHE 426  
/E LEU 427  
/E CYS 428  
/E LEU 431  
/E MET 434  
/E VAL 436  
/E GLN 437  
/E MET 440  
/E VAL 442  
/E ILE 443  
/E TYR 446  
/E ASN 447  
/E LEU 448  
/E LEU 449  
/E SER 451  
/E SER 452  
/E LEU 454  
/E VAL 455  
/E VAL 459  
/E VAL 461  
/E LEU 462  
/E LEU 463  
/E ILE 466  
/E GLN 467  
/E TYR 468  
/E ILE 470  
/E THR 472  
/E LYS 473  
/E GLU 476  
/E GLN 478  
/E THR 481  
/E LEU 482  
/E ASP 483  
/E TYR 484  
/E GLU 487  
/E LEU 489  
/E LYS 491  
/E THR 492  
/E ASN 493  
/E ILE 495  
/E LEU 496  
/E LYS 497  
/E LYS 500  
/E LEU 501  
/E LEU 502  
/E LYS 503  
/E LEU 504  
/E TYR 505  
/E GLU 508  
/E HIS 509  
/E PHE 511  
/E SER 514  
/E VAL 515  
/E GLU 516  
/E GLU 517  
/E ARG 519  
/E MET 520  
/E LYS 521  
/E GLU 522  
/E LEU 523  
/E LEU 526  
/E LYS 527  
/E PHE 529  
/E LEU 531  
/E THR 533  
/E SER 534  
/E MET 539  
/E ASN 540  
/E ILE 543  
/E ILE 545  
/E LEU 549  
/E THR 551  
/E THR 554  
/E TYR 557  
/E ASN 561  
/E ASN 562  
/E LEU 563  
/E LYS 564  
/E GLU 567  
/E PHE 569  
/E SER 571  
/E SER 573  
/E PHE 575  
/E ILE 577  
/E VAL 579  
/E LEU 584  
/E ARG 590  
/E LYS 594  
/E ILE 596  
/E ILE 597  
/E LYS 601  
/E ASN 603  
/E GLU 604  
/E LEU 607  
/E SER 608  
/E ASP 609  
/E GLU 610  
/E ILE 611  
/E GLU 613  
/E ASP 614  
/E SER 615  
/E TRP 616  
/E GLU 664  
/E ASP 665  
/E VAL 666  
/E ILE 668  
/E LYS 669  
/E ASN 672  
/E TYR 674  
/E PHE 675  
/E SER 676  
/E SER 679  
/E LEU 681  
/E THR 683  
/E LEU 684  
/E SER 685  
/E ASN 686  
/E ILE 687  
/E ASP 688  
/E ILE 689  
/E ARG 690  
/E THR 693  
/E GLN 695  
/E MET 698  
/E ILE 699  
/E VAL 700  
/E GLN 702  
/E VAL 703  
/E CYS 705  
/E SER 708  
/E SER 709  
/E LEU 710  
/E LEU 711  
/E LEU 712  
/E LEU 715  
/E GLU 717  
/E MET 718  
/E GLN 719  
/E THR 720  
/E LEU 721  
/E GLU 722  
/E LYS 724  
/E VAL 725  
/E TYR 726  
/E TRP 727  
/E ASN 728  
/E ASN 729  
/E VAL 730  
/E ASN 731  
/E GLU 732  
/E ARG 741  
/E SER 742  
/E ARG 743  
/E SER 744  
/E ARG 745  
/E TYR 746  
/E SER 747  
/E VAL 748  
/E LYS 754  
/E LEU 757  
/E LEU 758  
/E ASN 759  
/E THR 761  
/E VAL 762  
/E GLU 763  
/E GLU 764  
/E ASN 765  
/E THR 767  
/E PHE 768  
/E SER 770  
/E SER 771  
/E PHE 772  
/E ARG 774  
/E GLN 775  
/E THR 781  
/E ASP 782  
/E CYS 784  
/E LEU 786  
/E GLN 787  
/E ASP 789  
/E ILE 790  
/E ASP 791  
/E LEU 792  
/E LEU 793  
/E PHE 795  
/E ASP 797  
/E GLN 798  
/E THR 799  
/E GLU 800  
/E ILE 801  
/E GLU 803  
/E ARG 804  
/E ILE 806  
/E ASN 807  
/E LEU 808  
/E SER 809  
/E ARG 813  
/E GLN 814  
/E CYS 817  
/E ARG 820  
/E GLN 824  
/E THR 826  
/E ILE 828  
/E ASP 832  
/E LEU 838  
/E ASP 839  
/E ILE 840  
/E HIS 841  
/E LEU 842  
/E SER 843  
/E ASP 844  
/E HIS 845  
/E LEU 846  
/E MET 847  
/E GLN 848  
/E GLU 849  
/E ILE 851  
/E LEU 852  
/E LYS 853  
/E LEU 855  
/E ASP 857  
/E LYS 859  
/E ARG 860  
/E VAL 862  
/E VAL 863  
/E LEU 864  
/E VAL 865  
/E HIS 867  
/E LYS 868  
/E LEU 869  
/E GLN 870  
/E LEU 872  
/E HIS 874  
/E ASP 876  
/E ILE 878  
/E ILE 879  
/E MET 881  
/E LYS 882  
/E ASP 883  
/E SER 885  
/E VAL 886  
/E LEU 887  
/E ARG 888  
/E GLU 889  
/E THR 891  
/E LEU 892  
/E LYS 893  
/E ASP 894  
/E ILE 895  
/E GLN 896  
/E THR 897  
/E LYS 898  
/E ASP 899  
/E VAL 900  
/E GLU 901  
/E LEU 902  
/E TYR 903  
/E GLU 904  
/E HIS 905  
/E TRP 906  
/E LYS 907  
/E THR 908  
/E LEU 909  
/E MET 910  
/E ASP 961  
/E ASN 962  
/E MET 963  
/E SER 964  
/E THR 965  
/E VAL 966  
/E MET 967  
/E ARG 968  
/E LEU 969  
/E ARG 970  
/E THR 971  
/E LYS 972  
/E MET 973  
/E LYS 976  
/E TRP 980  
/E LEU 982  
/E SER 984  
/E PHE 987  
/E LEU 989  
/E LEU 990  
/E PHE 991  
/E LEU 992  
/E MET 993  
/E ILE 994  
/E PHE 995  
/E SER 996  
/E LEU 998  
/E LEU 999  
/E LYS 1000  
/E SER 1002  
/E VAL 1003  
/E ILE 1004  
/E VAL 1005  
/E ILE 1007  
/E ASP 1008  
/E TYR 1009  
/E TRP 1010  
/E THR 1013  
/E TRP 1014  
/E THR 1015  
/E SER 1016  
/E GLU 1017  
/E TYR 1018  
/E SER 1019  
/E ILE 1020  
/E ASN 1021  
/E ASP 1022  
/E LYS 1025  
/E ASP 1027  
/E GLN 1028  
/E TYR 1031  
/E PHE 1035  
/E SER 1036  
/E ILE 1037  
/E LEU 1038  
/E CYS 1039  
/E ILE 1043  
/E PHE 1044  
/E LEU 1045  
/E CYS 1046  
/E LEU 1047  
/E VAL 1048  
/E LEU 1051  
/E THR 1052  
/E VAL 1053  
/E GLU 1054  
/E TRP 1055  
/E MET 1056  
/E LEU 1058  
/E THR 1059  
/E LEU 1064  
/E HIS 1065  
/E ASN 1067  
/E LEU 1068  
/E LEU 1069  
/E ASN 1070  
/E LYS 1071  
/E ILE 1073  
/E LEU 1074  
/E ILE 1077  
/E ARG 1078  
/E PHE 1079  
/E ASP 1081  
/E THR 1082  
/E LEU 1085  
/E LEU 1087  
/E LEU 1089  
/E THR 1096  
/E ASP 1100  
/E ILE 1103  
/E GLU 1108  
/E LEU 1110  
/E THR 1111  
/E THR 1114  
/E LEU 1115  
/E LEU 1118  
/E ILE 1121  
/E MET 1123  
/E ILE 1124  
/E THR 1128  
/E VAL 1130  
/E PHE 1131  
/E LEU 1132  
/E ILE 1133  
/E LEU 1135  
/E LEU 1138  
/E VAL 1140  
/E PHE 1142  
/E TYR 1143  
/E PHE 1144  
/E ILE 1145  
/E GLN 1146  
/E LYS 1147  
/E ARG 1150  
/E VAL 1151  
/E SER 1153  
/E LYS 1154  
/E ASP 1155  
/E LEU 1156  
/E GLN 1157  
/E GLU 1158  
/E ASP 1160  
/E ASP 1161  
/E GLN 1164  
/E LEU 1165  
/E LEU 1167  
/E LEU 1168  
/E CYS 1169  
/E PHE 1171  
/E SER 1172  
/E GLU 1173  
/E THR 1174  
/E GLU 1176  
/E LEU 1178  
/E THR 1179  
/E THR 1180  
/E ARG 1182  
/E ARG 1185  
/E HIS 1186  
/E GLU 1187  
/E THR 1188  
/E ARG 1189  
/E PHE 1190  
/E LYS 1191  
/E GLN 1192  
/E GLU 1196  
/E ASP 1199  
/E THR 1200  
/E ASN 1202  
/E ILE 1203  
/E LEU 1206  
/E PHE 1207  
/E LEU 1208  
/E ASN 1212  
/E LEU 1215  
/E GLU 1216  
/E ARG 1218  
/E THR 1219  
/E ASP 1220  
/E LEU 1222  
/E ILE 1226  
/E LEU 1228  
/E ILE 1232  
/E SER 1234  
/E SER 1236  
/E SER 1238  
/E SER 1239  
/E ASN 1240  
/E SER 1241  
/E LEU 1243  
/E VAL 1244  
/E LEU 1246  
/E LEU 1248  
/E THR 1253  
/E ILE 1254  
/E ASN 1259  
/E VAL 1262  
/E LEU 1265  
/E ASP 1267  
/E LEU 1268  
/E GLU 1269  
/E GLN 1271  
/E MET 1272  
/E LYS 1276  
/E LYS 1277  
/E VAL 1278  
/E ASN 1279  
/E PHE 1281  
/E LEU 1282  
/E THR 1283  
/E MET 1284  
/E GLU 1285  
/E SER 1286  
/E GLU 1287  
/E ASN 1288  
/E TYR 1289  
/E GLU 1290  
/E THR 1292  
/E MET 1293  
/E ASP 1294  
/E SER 1296  
/E GLN 1297  
/E VAL 1298  
/E GLU 1300  
/E HIS 1301  
/E TRP 1302  
/E PRO 1303  
/E GLN 1304  
/E GLU 1305  
/E GLU 1307  
/E ILE 1308  
/E LYS 1309  
/E ILE 1310  
/E HIS 1311  
/E ASP 1312  
/E LEU 1313  
/E CYS 1314  
/E VAL 1315  
/E TYR 1317  
/E GLU 1318  
/E ASN 1319  
/E ASN 1320  
/E LEU 1321  
/E LYS 1322  
/E VAL 1324  
/E LEU 1325  
/E LYS 1326  
/E HIS 1327  
/E VAL 1328  
/E LYS 1329  
/E ILE 1332  
/E LYS 1333  
/E GLN 1336  
/E LYS 1337  
/E VAL 1338  
/E ILE 1340  
/E CYS 1341  
/E ARG 1343  
/E THR 1344  
/E SER 1346  
/E LYS 1348  
/E SER 1349  
/E SER 1350  
/E LEU 1351  
/E SER 1352  
/E LEU 1353  
/E PHE 1355  
/E PHE 1356  
/E ARG 1357  
/E MET 1358  
/E VAL 1359  
/E ASP 1360  
/E ILE 1361  
/E PHE 1362  
/E ASP 1363  
/E LYS 1365  
/E ILE 1366  
/E VAL 1367  
/E ILE 1368  
/E ASP 1369  
/E ASP 1372  
/E LYS 1375  
/E LEU 1376  
/E HIS 1379  
/E LEU 1381  
/E ARG 1384  
/E ILE 1387  
/E GLN 1390  
/E ASP 1391  
/E ILE 1393  
/E PHE 1395  
/E SER 1396  
/E SER 1398  
/E ILE 1399  
/E ARG 1400  
/E PHE 1401  
/E ASN 1402  
/E LEU 1403  
/E ASP 1404  
/E GLU 1406  
/E LYS 1408  
/E THR 1410  
/E ASP 1411  
/E ASP 1412  
/E ARG 1413  
/E LEU 1414  
/E TRP 1415  
/E GLU 1416  
/E LEU 1418  
/E GLU 1419  
/E ILE 1420  
/E GLN 1422  
/E LEU 1423  
/E LYS 1424  
/E ASN 1425  
/E MET 1426  
/E VAL 1427  
/E LYS 1428  
/E SER 1429  
/E LEU 1430  
/E LEU 1434  
/E ASP 1435  
/E GLU 1440  
/E GLU 1443  
/E ASN 1444  
/E PHE 1445  
/E SER 1446  
/E VAL 1447  
/E GLN 1449  
/E GLN 1451  
/E LEU 1452  
/E PHE 1453  
/E CYS 1454  
/E LEU 1455  
/E ARG 1457  
/E PHE 1459  
/E LEU 1466  
/E ILE 1467  
/E MET 1468  
/E ASP 1469  
/E GLU 1470  
/E ILE 1475  
/E ASP 1476  
/E MET 1477  
/E GLU 1480  
/E ILE 1482  
/E GLN 1484  
/E LYS 1485  
/E VAL 1486  
/E MET 1488  
/E PHE 1491  
/E ARG 1494  
/E THR 1495  
/E THR 1498  
/E ILE 1499  
/E ARG 1502  
/E VAL 1503  
/E HIS 1504  
/E THR 1505  
/E ILE 1506  
/E LEU 1507  
/E ASP 1510  
/E LEU 1511  
/E VAL 1512  
/E ILE 1513  
/E MET 1515  
/E LYS 1516  
/E ARG 1517  
/E ASN 1519  
/E ILE 1520  
/E LEU 1521  
/E GLU 1522  
/E TYR 1523  
/E ASP 1524  
/E THR 1525  
/E GLU 1527  
/E SER 1528  
/E LEU 1529  
/E LEU 1530  
/E GLN 1532  
/E GLU 1533  
/E ASP 1534  
/E PHE 1537  
/E SER 1539  
/E PHE 1540  
/E VAL 1541  
/E ARG 1542  
/G LEU 3  
/G ASN 8  
/G ILE 10  
/G TYR 13  
/G ASN 14  
/G ILE 15  
/G TYR 16  
/G HIS 17  
/G VAL 19  
/G LEU 20  
/G GLN 21  
/G PHE 25  
/G VAL 26  
/G ASP 27  
/G ASN 30  
/G VAL 32  
/G VAL 35  
/G PHE 36  
/G LEU 37  
/G LEU 38  
/G ILE 40  
/G PHE 42  
/G ILE 44  
/G LEU 45  
/G ILE 47  
/G TRP 49  
/G SER 51  
/G GLN 52  
/G SER 53  
/G SER 54  
/G LYS 55  
/G VAL 56  
/G GLN 57  
/G ILE 58  
/G HIS 59  
/G HIS 60  
/G ASN 61  
/G THR 62  
/G TRP 63  
/G LEU 64  
/G HIS 65  
/G PHE 66  
/G ASN 70  
/G LEU 71  
/G ARG 72  
/G ILE 74  
/G LEU 75  
/G PHE 77  
/G CYS 85  
/G GLU 86  
/G ILE 87  
/G GLU 89  
/G ILE 91  
/G VAL 92  
/G SER 93  
/G SER 95  
/G GLN 96  
/G SER 99  
/G ARG 100  
/G HIS 103  
/G MET 106  
/G THR 115  
/G SER 118  
/G ILE 119  
/G ILE 125  
/G GLU 126  
/G THR 127  
/G ASN 129  
/G LEU 135  
/G PHE 138  
/G LEU 139  
/G TYR 140  
/G VAL 142  
/G MET 143  
/G ILE 146  
/G LYS 148  
/G ILE 150  
/G LYS 151  
/G VAL 153  
/G LYS 154  
/G TRP 156  
/G GLN 157  
/G LEU 158  
/G TRP 160  
/G MET 162  
/G SER 163  
/G ASP 164  
/G LEU 165  
/G CYS 168  
/G ILE 169  
/G ILE 175  
/G LEU 176  
/G LEU 179  
/G LEU 180  
/G MET 181  
/G VAL 183  
/G GLU 184  
/G ILE 185  
/G ASN 186  
/G VAL 187  
/G ILE 188  
/G VAL 190  
/G ARG 191  
/G ARG 192  
/G TYR 193  
/G VAL 194  
/G PHE 195  
/G PHE 196  
/G MET 197  
/G ASN 198  
/G GLN 200  
/G LYS 201  
/G VAL 202  
/G LYS 203  

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue HIS (net charge -3) with am1-bcc method  
Running ANTECHAMBER command:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/antechamber
-ek qm_theory='AM1', -i
/var/folders/7p/ktsg_gbs0db8d6sp4ccqcvdh0000gn/T/tmphldwj17h/ante.in.mol2 -fi
mol2 -o
/var/folders/7p/ktsg_gbs0db8d6sp4ccqcvdh0000gn/T/tmphldwj17h/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n  
(HIS) ``  
(HIS) `Welcome to antechamber 20.0: molecular input file processor.`  
(HIS) ``  
(HIS) `Info: Finished reading file
(/var/folders/7p/ktsg_gbs0db8d6sp4ccqcvdh0000gn/T/tmphldwj17h/ante.in.mol2);
atoms read (22), bonds read (21).`  
(HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(HIS) `Running:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/bondtype -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(HIS) ``  
(HIS) ``  
(HIS) `Running:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(HIS) `Info: Total number of electrons: 86; net charge: -3`  
(HIS) ``  
(HIS) `Running:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out`  
(HIS) ``  
(HIS) `Running:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(HIS) ``  
(HIS) `Running:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/atomtype -f
ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(HIS) ``  
Charges for residue HIS determined  
Assigning partial charges to residue HIS+HIS (net charge -6) with am1-bcc
method  
Running ANTECHAMBER command:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/antechamber
-ek qm_theory='AM1', -i
/var/folders/7p/ktsg_gbs0db8d6sp4ccqcvdh0000gn/T/tmp1f8nl4q_/ante.in.mol2 -fi
mol2 -o
/var/folders/7p/ktsg_gbs0db8d6sp4ccqcvdh0000gn/T/tmp1f8nl4q_/ante.out.mol2 -fo
mol2 -c bcc -nc -6 -j 5 -s 2 -dr n  
(HIS+HIS) ``  
(HIS+HIS) `Welcome to antechamber 20.0: molecular input file processor.`  
(HIS+HIS) ``  
(HIS+HIS) `Info: Finished reading file
(/var/folders/7p/ktsg_gbs0db8d6sp4ccqcvdh0000gn/T/tmp1f8nl4q_/ante.in.mol2);
atoms read (26), bonds read (25).`  
(HIS+HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(HIS+HIS) `Running:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/bondtype -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(HIS+HIS) ``  
(HIS+HIS) ``  
(HIS+HIS) `Running:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(HIS+HIS) `Info: Total number of electrons: 116; net charge: -6`  
(HIS+HIS) ``  
(HIS+HIS) `Running:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out`  
(HIS+HIS)
`/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`  
(HIS+HIS) `Cannot properly run
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out".`  
Failure running ANTECHAMBER for residue HIS+HIS Check reply log for details  




OpenGL version: 4.1 ATI-4.6.20
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,3
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 1554.140.20.0.0 (iBridge: 18.16.14759.0.1,0)

Software:

    System Software Overview:

      System Version: macOS 11.6 (20G165)
      Kernel Version: Darwin 20.6.0
      Time since boot: 12 days 16:34

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2

    Radeon Pro Vega 20:

      Chipset Model: Radeon Pro Vega 20
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x69af
      Revision ID: 0x00c0
      ROM Revision: 113-D2060I-087
      VBIOS Version: 113-D20601MA0T-016
      Option ROM Version: 113-D20601MA0T-016
      EFI Driver Version: 01.01.087
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.0
    charset-normalizer: 2.0.6
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.30.1
    ChimeraX-AtomicLibrary: 4.1.4
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202110062055
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.1
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.1
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2
    ChimeraX-ModelPanel: 1.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-Phenix: 0.3
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.2
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.10.0
    Cython: 0.29.24
    decorator: 5.1.0
    distlib: 0.3.2
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.4.0
    html2text: 2020.1.16
    idna: 3.2
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    joblib: 1.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.8.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
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[Tom Goddard]

On older ChimeraX 1.2.5 it also fails, much faster in seconds, not sure if on the same ligand, #5415.

[pett]

Due to the massive number of incomplete residues in this structure, there isn't a lot of motivation to get coulombic to "succeed" on this structure. The NIH3D pipeline script will be modified to skip coulombic output for structures with large numbers of incomplete residues.

[goddard@…]

I'd suggest closing this as a limitation.  It is an sqm and AmberTools problem so how would we be able to fix it?