stefdoerr
commented
4 months ago Hi, and thanks for finding this bug!
Once this job here completes https://github.com/Acellera/moleculekit/actions/runs/8045964937 there will be a new moleculekit release available, version 1.8.22. Upgrade to that one and it will work (sort of because it will throw a new error about a unknown residue called RU3 in your input structure). The RNA will require some digging around to find parameters/topologies for it's residues.
vas2201
Hello,
I encountered an error while running the code provided below. Could you please advise on how to resolve this issue?
mol = Molecule('2LEB')
mol.filter("protein")
mol.set('segid', 'A', sel='protein')
mol_op = systemPrepare(mol) mol_seg = autoSegment(mol_op) mol_solv = solvate (mol_seg, pad=10) mol_amber = amber.build(mol_solv, saltconc = 0.15, outdir='build-amber')
---- Molecule chain report ---- Chain A: First residue: MET 1
Final residue: SER 101
Chain B: First residue: U 102
Final residue: U 107
---- End of chain report ----
2024-02-26 01:48:02,253 - moleculekit.tools.preparation - INFO - Modified residue HIS 63 A to HIE 2024-02-26 01:48:02,254 - moleculekit.tools.preparation - INFO - Modified residue HIS 99 A to HIE 2024-02-26 01:48:02,254 - moleculekit.tools.preparation - INFO - Modified residue HIS 100 A to HIE 2024-02-26 01:48:02,254 - moleculekit.tools.preparation - INFO - Modified residue U 102 B to RU5 2024-02-26 01:48:02,255 - moleculekit.tools.preparation - INFO - Modified residue C 103 B to RC 2024-02-26 01:48:02,255 - moleculekit.tools.preparation - INFO - Modified residue C 104 B to RC 2024-02-26 01:48:02,256 - moleculekit.tools.preparation - INFO - Modified residue A 105 B to RA 2024-02-26 01:48:02,256 - moleculekit.tools.preparation - INFO - Modified residue G 106 B to RG 2024-02-26 01:48:02,257 - moleculekit.tools.preparation - INFO - Modified residue U 107 B to RU3 2024-02-26 01:48:02,269 - htmd.builder.solvate - INFO - Using water pdb file at: /home/nmrbox/spenumutchu/anaconda3/envs/htmd2/lib/python3.10/site-packages/htmd/share/solvate/wat.pdb 2024-02-26 01:48:02,850 - htmd.builder.solvate - INFO - Replicating 4 water segments, 2 by 1 by 2 Solvating: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 4/4 [00:01<00:00, 3.06it/s] 2024-02-26 01:48:04,163 - htmd.builder.solvate - INFO - 5427 water molecules were added to the system. 2024-02-26 01:48:04,442 - htmd.builder.builder - WARNING - Segments ['P0'] contain both protein and non-protein atoms. Please assign separate segments to them or the build procedure might fail. 2024-02-26 01:48:04,942 - py.warnings - WARNING - /home/nmrbox/spenumutchu/anaconda3/envs/htmd2/lib/python3.10/site-packages/moleculekit/align.py:52: RuntimeWarning: Mean of empty slice. centroidP = P.mean(axis=0)
2024-02-26 01:48:04,942 - py.warnings - WARNING - /home/nmrbox/spenumutchu/anaconda3/envs/htmd2/lib/python3.10/site-packages/numpy/core/_methods.py:184: RuntimeWarning: invalid value encountered in divide ret = um.true_divide(
2024-02-26 01:48:04,943 - py.warnings - WARNING - /home/nmrbox/spenumutchu/anaconda3/envs/htmd2/lib/python3.10/site-packages/moleculekit/align.py:53: RuntimeWarning: Mean of empty slice. centroidQ = Q.mean(axis=0)
2024-02-26 01:48:04,943 - py.warnings - WARNING - /home/nmrbox/spenumutchu/anaconda3/envs/htmd2/lib/python3.10/site-packages/moleculekit/align.py:27: RuntimeWarning: invalid value encountered in scalar divide RMSD = np.sqrt(np.abs(RMSD / P.shape[0]))
IndexError Traceback (most recent call last) Cell In[35], line 7 5 mol_seg = autoSegment(mol_op) 6 mol_solv = solvate (mol_seg, pad=10) ----> 7 mol_amber = amber.build(mol_solv, saltconc = 0.15, outdir='build-amber')
File ~/anaconda3/envs/htmd2/lib/python3.10/site-packages/htmd/builder/amber.py:703, in build(mol, ff, topo, param, prefix, outdir, caps, ionize, saltconc, saltanion, saltcation, disulfide, teleap, teleapimports, execute, atomtypes, offlibraries, gbsa, igb) 697 if all(ff19tip3p): 698 logger.warning( 699 "CAUTION: AMBER Forcefield ff19SB is NOT compatible with TIP3P water model." 700 " Consider using ff14SB instead or using the OPC water model." 701 ) --> 703 disulfide = _prepareMolecule(mol, caps, disulfide) 704 _detect_cofactors_ncaa_ptm(mol, param, topo) 706 if ionize:
File ~/anaconda3/envs/htmd2/lib/python3.10/site-packages/htmd/builder/amber.py:523, in _prepareMolecule(mol, caps, disulfide) 520 logger.info(f"Found cyclic segment {cc}. Disabling capping on it.") 521 del caps[cc] --> 523 _add_caps(mol, caps) 525 # Before modifying the resids copy the molecule to map back the disulfide bonds 526 mol_orig_resid = mol.copy()
File ~/anaconda3/envs/htmd2/lib/python3.10/site-packages/htmd/builder/amber.py:1099, in _add_caps(mol, caps) 1097 capmol.resid[:] += terminals[term]["resid"] 1098 capmol.chain[:] = mol.chain[mask][0] -> 1099 capmol.remove(cap_idx, _logger=False) # Remove atoms which were aligned 1101 # Remove the atoms defined in remove_atoms to clean up the termini 1102 removed = mol.remove( 1103 np.isin(mol.name, remove_atoms[cap]) & mask, _logger=False 1104 )
File ~/anaconda3/envs/htmd2/lib/python3.10/site-packages/moleculekit/molecule.py:608, in Molecule.remove(self, selection, _logger) 606 self._updateBondsAnglesDihedrals(sel) 607 for k in self._atom_and_coord_fields: --> 608 self.dict[k] = np.delete(self.dict[k], sel, axis=0) 609 if k == "coords": 610 self.dict[k] = np.atleast_3d(self.dict[k])
File <__array_function__ internals>:200, in delete(*args, **kwargs)
File ~/anaconda3/envs/htmd2/lib/python3.10/site-packages/numpy/lib/function_base.py:5235, in delete(arr, obj, axis) 5233 else: 5234 keep = ones(N, dtype=bool) -> 5235 keep[obj,] = False 5237 slobj[axis] = keep 5238 new = arr[tuple(slobj)]
IndexError: arrays used as indices must be of integer (or boolean) type