(Seems like the attachment didn’t make it through in my earlier message, so sending again with inline files)
Running MCPB.py -i Rh-paddlewheel.in -s 1 with the files below produces the error:
File "/share/apps/amber/20.11/openmpi/intel/lib/python3.8/site-packages/pymsmt/mcpb/gene_model_files.py", line 1380, in build_small_model
AtNum = Atnum[gatm.element]
KeyError: 'R'
I am guessing there is some formatting issue in the mol2 files, but can’t identify it. Could also be pdb, but really not sure where to look. Could it be a justification issue in the pdb file?
Any suggestions?
All relevant files are attached.
Thank you
Alexej
——Rh-paddlewheel.in ----
original_pdb Rh-paddlewheel3_numbered_edit2.pdb
group_name Rh-paddlewheel
ion_ids 1 2
ion_mol2files RH.mol2
naa_mol2files RES.mol2
frcmod_files ligand.frcmod
——RH.mol2 ----
.<TRIPOS>MOLECULE
2 1 1 0 0
SMALL
User Assigned Charge
.<TRIPOS>ATOM
1 Rh1 -5.1960 -0.0390 -1.2340 RH 1 RH 2.000000
2 Rh2 -3.3050 0.8830 -0.0770 RH 1 RH 2.000000
.<TRIPOS>BOND
.<TRIPOS>SUBSTRUCTURE
1 RH 1 TEMP 0 **** **** 0 ROOT
—RES.mol2—
.<TRIPOS>MOLECULE
pdb_files/Rh-ligands.pdb
34 28 0 0 0
SMALL
GASTEIGER
.<TRIPOS>ATOM
1 O1 -4.0290 2.6200 -0.3000 o 2 RES -0.2467
2 O2 -1.8020 1.6490 0.8160 OW 2 RES -0.4105
3 H1 -1.2440 0.9450 1.1630 HW 2 RES 0.2052
4 O3 -4.3420 0.6930 1.5270 o 2 RES -0.2467
5 O4 -2.5780 -0.8640 0.1590 o 2 RES -0.2467
6 O5 -2.4430 0.9880 -1.7840 o 2 RES -0.2467
7 O6 -5.9700 -0.5350 0.4170 o 2 RES -0.2467
8 O7 -5.9910 1.6940 -1.1020 o 2 RES -0.2467
9 O8 -4.4110 0.4890 -2.9000 o 2 RES -0.2467
10 O9 -6.5790 -0.8780 -2.2540 OW 2 RES -0.4105
11 H2 -6.3620 -0.8300 -3.1860 HW 2 RES 0.2052
12 O10 -4.2140 -1.6860 -1.2450 o 2 RES -0.2467
13 C1 -5.2810 2.7440 -0.7070 c 2 RES 0.3530
14 C2 -5.9340 4.1370 -0.7220 c3 2 RES 0.0375
15 H3 -5.1900 4.8810 -0.9140 hc 2 RES 0.0343
16 H4 -6.6730 4.1700 -1.4900 hc 2 RES 0.0343
17 H5 -6.3930 4.3250 0.2300 hc 2 RES 0.0343
18 C3 -5.4600 -0.0330 1.5340 c 2 RES 0.3530
19 C4 -3.1360 0.8460 -2.9130 c 2 RES 0.3530
20 C5 -3.1180 -1.8550 -0.5170 c 2 RES 0.3530
21 C6 -2.4600 -3.2440 -0.4620 c3 2 RES 0.0375
22 H6 -1.9770 -3.3760 0.4800 hc 2 RES 0.0343
23 H7 -3.2070 -3.9950 -0.5900 hc 2 RES 0.0343
24 H8 -1.7380 -3.3280 -1.2390 hc 2 RES 0.0343
25 C7 -2.4400 1.1020 -4.2650 c3 2 RES 0.0375
26 H9 -2.0130 0.1860 -4.6290 hc 2 RES 0.0343
27 H10 -3.1590 1.4720 -4.9710 hc 2 RES 0.0343
28 H11 -1.6610 1.8280 -4.1360 hc 2 RES 0.0343
29 C8 -6.1730 -0.2910 2.8710 c3 2 RES 0.0375
30 H12 -6.6890 -1.2270 2.8260 hc 2 RES 0.0343
31 H13 -5.4470 -0.3180 3.6570 hc 2 RES 0.0343
32 H14 -6.8760 0.4950 3.0620 hc 2 RES 0.0343
33 H15 -2.1080 2.2010 1.5410 HW 2 RES 0.2052
34 H16 -7.4140 -0.4250 -2.0930 HW 2 RES 0.2052
.<TRIPOS>BOND
1 27 25 1
2 26 25 1
3 25 28 1
4 25 19 1
5 11 10 1
6 19 9 ar
7 19 6 ar
8 10 34 1
9 16 14 1
10 12 20 ar
11 24 21 1
12 8 13 ar
13 15 14 1
14 14 13 1
15 14 17 1
16 13 1 ar
17 23 21 1
18 20 21 1
19 20 5 ar
20 21 22 1
21 7 18 ar
22 2 3 1
23 2 33 1
24 4 18 ar
25 18 29 1
26 30 29 1
27 29 32 1
28 29 31 1
.<TRIPOS>SUBSTRUCTURE
1 RES 1 TEMP 0 **** **** 0 ROOT
---Rh-paddlewheel3_numbered_edit2.pdb—
HETATM 1 Rh1 RH 1 -5.196 -0.039 -1.234
HETATM 2 Rh2 RH 1 -3.305 0.883 -0.077
HETATM 3 O1 RES 2 -4.029 2.620 -0.300
HETATM 4 O2 RES 2 -1.802 1.649 0.816
HETATM 5 H1 RES 2 -1.244 0.945 1.163
HETATM 6 O3 RES 2 -4.342 0.693 1.527
HETATM 7 O4 RES 2 -2.578 -0.864 0.159
HETATM 8 O5 RES 2 -2.443 0.988 -1.784
HETATM 9 O6 RES 2 -5.970 -0.535 0.417
HETATM 10 O7 RES 2 -5.991 1.694 -1.102
HETATM 11 O8 RES 2 -4.411 0.489 -2.900
HETATM 12 O9 RES 2 -6.579 -0.878 -2.254
HETATM 13 H2 RES 2 -6.362 -0.830 -3.186
HETATM 14 O10 RES 2 -4.214 -1.686 -1.245
HETATM 15 C1 RES 2 -5.281 2.744 -0.707
HETATM 16 C2 RES 2 -5.934 4.137 -0.722
HETATM 17 H3 RES 2 -5.190 4.881 -0.914
HETATM 18 H4 RES 2 -6.673 4.170 -1.490
HETATM 19 H5 RES 2 -6.393 4.325 0.230
HETATM 20 C3 RES 2 -5.460 -0.033 1.534
HETATM 21 C4 RES 2 -3.136 0.846 -2.913
HETATM 22 C5 RES 2 -3.118 -1.855 -0.517
HETATM 23 C6 RES 2 -2.460 -3.244 -0.462
HETATM 24 H6 RES 2 -1.977 -3.376 0.480
HETATM 25 H7 RES 2 -3.207 -3.995 -0.590
HETATM 26 H8 RES 2 -1.738 -3.328 -1.239
HETATM 27 C7 RES 2 -2.440 1.102 -4.265
HETATM 28 H9 RES 2 -2.013 0.186 -4.629
HETATM 29 H10 RES 2 -3.159 1.472 -4.971
HETATM 30 H11 RES 2 -1.661 1.828 -4.136
HETATM 31 C8 RES 2 -6.173 -0.291 2.871
HETATM 32 H12 RES 2 -6.689 -1.227 2.826
HETATM 33 H13 RES 2 -5.447 -0.318 3.657
HETATM 34 H14 RES 2 -6.876 0.495 3.062
HETATM 35 H15 RES 2 -2.108 2.201 1.541
HETATM 36 H16 RES 2 -7.414 -0.425 -2.093
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Received on Fri Feb 04 2022 - 06:30:02 PST
