vas2201
commented
8 months ago Looks like I can use amber force field . I have come across a resource provided by Dimitris's Group via the following link, which includes libraries, definitions, frcmod files, and sample input files for the modified ARG amino acid: http://pc164.materials.uoi.gr/dpapageo/amberparams.php However, I am uncertain about the process of copying or updating these libraries and frcmod files to the original files. If possible, could you please offer guidance and suggestions on how to update these parameters effectively? Thank you very much for your assistance.
stefdoerr
Hi, I'm in search of force-field parameters for methyl modification of ARG (attached screenshot for your reference). Screenshot : (https://github.com/Acellera/htmd/assets/29959559/9edca9ad-6a46-4b1c-bd1c-3cf4f96846be)
Thus far, I've identified parameters for symmetrical dimethylated ARG (sDMA) in CHARMM (as DA2). However, I haven't found parameters for monomethylated ARG (MMA) or asymmetrical dimethylated ARG (aDMA). If you or someone you know has generated or worked on parameters for other types (MMA, aDMA).
I changed the specific ARG to DA2 ( symmetrical dimethylated ) and build the system using chramm force field. I am getting the following error. please advise on this matter.
mol = Molecule('step1_pdbreader.pdb') 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 = charmm.build(mol_solv, saltconc = 0.15, outdir='build-charmm', ignore_ns_errors = 'True')
Regards Vas
ERROR : 2024-03-22 00:25:51,946 - moleculekit.readers - WARNING - Atoms with names "HE21" "HE22" were guessed as element H but could also be He (helium). If this is a case, you can correct them with mol.set('element', 'He', sel='name "HE21" "HE22"') 2024-03-22 00:25:51,947 - moleculekit.readers - WARNING - Atoms with names "HG11" "HG12" "HG13" "HG21" "HG22" "HG23" were guessed as element H but could also be Hg (mercury). If this is a case, you can correct them with mol.set('element', 'Hg', sel='name "HG11" "HG12" "HG13" "HG21" "HG22" "HG23"') 2024-03-22 00:25:52,010 - moleculekit.molecule - INFO - Removed 24 atoms. 4650 atoms remaining in the molecule.
---- Molecule chain report ---- Chain P: First residue: MET 1
Final residue: ARG 319
---- End of chain report ----
ModuleNotFoundError Traceback (most recent call last) File ~/anaconda3/envs/htmd2/lib/python3.10/site-packages/moleculekit/tools/preparation.py:118, in _generate_nonstandard_residues_ff(mol, definition, forcefield, _molkit_ff, outdir, ignore_ns_errors, residue_smiles) 117 try: --> 118 from aceprep.prepare import rdk_prepare 119 except ImportError:
ModuleNotFoundError: No module named 'aceprep'
During handling of the above exception, another exception occurred:
RuntimeError Traceback (most recent call last) Cell In[11], line 4 2 mol.filter("protein") 3 mol.set('segid', 'A', sel='protein') ----> 4 mol_op = systemPrepare(mol) 5 mol_seg = autoSegment(mol_op) 6 mol_solv = solvate (mol_seg, pad=10)
File ~/anaconda3/envs/htmd2/lib/python3.10/site-packages/moleculekit/tools/preparation.py:734, in systemPrepare(mol_in, titration, pH, force_protonation, no_opt, no_prot, no_titr, hold_nonpeptidic_bonds, verbose, return_details, hydrophobic_thickness, plot_pka, ignore_ns_errors, _logger_level, _molkit_ff, outdir, residue_smiles) 731 _fix_protonation_resnames(mol_in) 733 definition, forcefield = _get_custom_ff(molkit_ff=_molkit_ff) --> 734 definition, forcefield = _generate_nonstandard_residues_ff( 735 mol_in, 736 definition, 737 forcefield, 738 _molkit_ff, 739 outdir, 740 ignore_ns_errors=ignore_ns_errors, 741 residue_smiles=residue_smiles, 742 ) 744 nonpept = None 745 if hold_nonpeptidic_bonds:
File ~/anaconda3/envs/htmd2/lib/python3.10/site-packages/moleculekit/tools/preparation.py:122, in _generate_nonstandard_residues_ff(mol, definition, forcefield, _molkit_ff, outdir, ignore_ns_errors, residue_smiles) 120 if ignore_ns_errors: 121 return definition, forcefield --> 122 raise RuntimeError( 123 "To protonate non-canonical aminoacids you need the aceprep library. Please contact Acellera info@acellera.com for more information or set ignore_ns_errors=True to ignore non-canonical residues in the protonation (this will leave the residues unprotonated)." 124 ) 126 with tempfile.TemporaryDirectory() as tmpdir: 127 for res in not_in_ff:
RuntimeError: To protonate non-canonical aminoacids you need the aceprep library. Please contact Acellera info@acellera.com for more information or set ignore_ns_errors=True to ignore non-canonical residues in the protonation (this will leave the residues unprotonated).