restraints for D3O+ give problems to run in phenix.refine
hello, apologies if this problem has already been reported, i browsed for a while and i am running out of ideas to solve my problem. i have a neutron structure i was refining fine with phenix.refine untill i had to add a D3O water. description: running phenix.elbow or phenix.refine with .cif file for D3O i am getting the following error: ... Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" O D3O W 1 " occ=0.53 ... (2 atoms not shown) pdb=" D3 D3O W 1 " occ=0.53 Number of atoms with unknown nonbonded energy type symbols: 3 "HETATM 2 D1 D3O W 1 .*. D " "HETATM 3 D2 D3O W 1 .*. D " "HETATM 4 D3 D3O W 1 .*. D " Time building chain proxies: 0.01, per 1000 atoms: 2.50 Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 3 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Also note that phenix.ready_set and phenix.elbow are available for creating restraint definitions (CIF files). ******************* i then modified the .param file implementing the apply_cif_modification and apply_cif_link parameters: refinement { main { number_of_macro_cycles = 10 ordered_solvent= false scattering_table= neutron } hydrogens { refine= individual } pdb_interpretation.apply_cif_modification { data_mod = D3O residue_selection = resname D3O } pdb_interpretation.apply_cif_link { data_link = D3O residue_selection_1 = chain W and resname D3O } } ... ************************** the .cif file i have was created with phenix.ready_set: ( i added first line after it failed without) data_mod_D3O # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level D3O D3O Unknown ligand 4 1 . # data_comp_D3O # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z D3O O O O -0.475 -12.5180 -14.4044 -43.0985 D3O H1 D D -0.294 -11.4013 -13.8002 -42.6392 D3O H2 D D -0.294 -13.3333 -13.3284 -43.0933 D3O H3 D D 0.063 -12.3324 -14.5311 -44.0190 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd D3O O H1 single 1.350 0.040 D3O O H2 single 1.350 0.040 D3O O H3 single 0.947 0.010 # loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd D3O H2 O H1 98.14 3.000 D3O H3 O H1 103.20 1.194 D3O H3 O H2 103.22 1.252 ********************************** whatever i do i systematically get the same error: Monomer Library directory: "/usr/local/phenix-1.7.1-743/chem_data/mon_lib" Total number of atoms: 1165 Number of models: 1 apply_cif_modification: data_mod: D3O Sorry: Missing CIF modification: data_mod_D3O Please check for spelling errors or specify the file name with the modification as an additional argument. ******************************** the command i enter is: phenix.refine xxxx.pdb xxxx.mtz D3O.ligands.cif high_res_xxxx-neutron-long-D3O.params \ refinement.input.xray_data.labels='IMEAN,SIGIMEAN' i looked in the online phenix.refine manual but it is not mentionning what to do in such error case. where should i put "data_mod_D3O" in the parameter file? is it the real source of the error? Could someone help me figuring out a solution to get the restraints to work for D3O(+), please? Maxime
Hi Maxime, Try changing energy type symbol in the cif file to H instead of D. E.g " 3O H1 D H -0.294 -11.4013 -13.8002 -42.6392" I would leave the cif_link out, it should not be necessary if the D3O+ is not covalently linked to the protein... HTH, Esko On 22.7.2011, at 16.52, Maxime Cuypers wrote:
hello,
apologies if this problem has already been reported, i browsed for a while and i am running out of ideas to solve my problem. i have a neutron structure i was refining fine with phenix.refine untill i had to add a D3O water.
description:
running phenix.elbow or phenix.refine with .cif file for D3O i am getting the following error: ... Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" O D3O W 1 " occ=0.53 ... (2 atoms not shown) pdb=" D3 D3O W 1 " occ=0.53 Number of atoms with unknown nonbonded energy type symbols: 3 "HETATM 2 D1 D3O W 1 .*. D " "HETATM 3 D2 D3O W 1 .*. D " "HETATM 4 D3 D3O W 1 .*. D " Time building chain proxies: 0.01, per 1000 atoms: 2.50
Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 3 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Also note that phenix.ready_set and phenix.elbow are available for creating restraint definitions (CIF files). *******************
i then modified the .param file implementing the apply_cif_modification and apply_cif_link parameters:
refinement { main { number_of_macro_cycles = 10 ordered_solvent= false scattering_table= neutron } hydrogens { refine= individual } pdb_interpretation.apply_cif_modification { data_mod = D3O residue_selection = resname D3O } pdb_interpretation.apply_cif_link { data_link = D3O residue_selection_1 = chain W and resname D3O } } ... **************************
the .cif file i have was created with phenix.ready_set: ( i added first line after it failed without)
data_mod_D3O # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level D3O D3O Unknown ligand 4 1 . # data_comp_D3O # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z D3O O O O -0.475 -12.5180 -14.4044 -43.0985 D3O H1 D D -0.294 -11.4013 -13.8002 -42.6392 D3O H2 D D -0.294 -13.3333 -13.3284 -43.0933 D3O H3 D D 0.063 -12.3324 -14.5311 -44.0190 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd D3O O H1 single 1.350 0.040 D3O O H2 single 1.350 0.040 D3O O H3 single 0.947 0.010 # loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd D3O H2 O H1 98.14 3.000 D3O H3 O H1 103.20 1.194 D3O H3 O H2 103.22 1.252
**********************************
whatever i do i systematically get the same error:
Monomer Library directory: "/usr/local/phenix-1.7.1-743/chem_data/mon_lib" Total number of atoms: 1165 Number of models: 1 apply_cif_modification: data_mod: D3O
Sorry: Missing CIF modification: data_mod_D3O Please check for spelling errors or specify the file name with the modification as an additional argument. ********************************
the command i enter is: phenix.refine xxxx.pdb xxxx.mtz D3O.ligands.cif high_res_xxxx- neutron-long-D3O.params \ refinement.input.xray_data.labels='IMEAN,SIGIMEAN'
i looked in the online phenix.refine manual but it is not mentionning what to do in such error case. where should i put "data_mod_D3O" in the parameter file? is it the real source of the error?
Could someone help me figuring out a solution to get the restraints to work for D3O(+), please?
Maxime _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Esko Oksanen, PhD Post-doctoral Fellow (EMBO) Groupe Synchrotron, Institut de Biologie Structurale J.P. Ebel 41, rue Jules Horowitz F-38027 GRENOBLE Cedex 1 FRANCE tel. +33 4 38 78 95 96 mob. +33 6 84 15 14 88
Maxime
Sorry but the D1, D2, D3 atom names in the PDB are supposed to be
matched automatically to the H1, H2, H3 names in the CIF restraints
file by phenix.refine. To get going you can edit the CIF restraints
and change the H1 to D1 etc. Changing the names in the PDB from D1 to
H1 would also work, but the former seems like the preferable option.
Nigel
On Fri, Jul 22, 2011 at 7:52 AM, Maxime Cuypers
hello,
apologies if this problem has already been reported, i browsed for a while and i am running out of ideas to solve my problem. i have a neutron structure i was refining fine with phenix.refine untill i had to add a D3O water.
description:
running phenix.elbow or phenix.refine with .cif file for D3O i am getting the following error: ... Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" O D3O W 1 " occ=0.53 ... (2 atoms not shown) pdb=" D3 D3O W 1 " occ=0.53 Number of atoms with unknown nonbonded energy type symbols: 3 "HETATM 2 D1 D3O W 1 .*. D " "HETATM 3 D2 D3O W 1 .*. D " "HETATM 4 D3 D3O W 1 .*. D " Time building chain proxies: 0.01, per 1000 atoms: 2.50
Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 3 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Also note that phenix.ready_set and phenix.elbow are available for creating restraint definitions (CIF files). *******************
i then modified the .param file implementing the apply_cif_modification and apply_cif_link parameters:
refinement { main { number_of_macro_cycles = 10 ordered_solvent= false scattering_table= neutron } hydrogens { refine= individual } pdb_interpretation.apply_cif_modification { data_mod = D3O residue_selection = resname D3O } pdb_interpretation.apply_cif_link { data_link = D3O residue_selection_1 = chain W and resname D3O } } ... **************************
the .cif file i have was created with phenix.ready_set: ( i added first line after it failed without)
data_mod_D3O # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level D3O D3O Unknown ligand 4 1 . # data_comp_D3O # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z D3O O O O -0.475 -12.5180 -14.4044 -43.0985 D3O H1 D D -0.294 -11.4013 -13.8002 -42.6392 D3O H2 D D -0.294 -13.3333 -13.3284 -43.0933 D3O H3 D D 0.063 -12.3324 -14.5311 -44.0190 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd D3O O H1 single 1.350 0.040 D3O O H2 single 1.350 0.040 D3O O H3 single 0.947 0.010 # loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd D3O H2 O H1 98.14 3.000 D3O H3 O H1 103.20 1.194 D3O H3 O H2 103.22 1.252
**********************************
whatever i do i systematically get the same error:
Monomer Library directory: "/usr/local/phenix-1.7.1-743/chem_data/mon_lib" Total number of atoms: 1165 Number of models: 1 apply_cif_modification: data_mod: D3O
Sorry: Missing CIF modification: data_mod_D3O Please check for spelling errors or specify the file name with the modification as an additional argument. ********************************
the command i enter is: phenix.refine xxxx.pdb xxxx.mtz D3O.ligands.cif high_res_xxxx-neutron-long-D3O.params \ refinement.input.xray_data.labels='IMEAN,SIGIMEAN'
i looked in the online phenix.refine manual but it is not mentionning what to do in such error case. where should i put "data_mod_D3O" in the parameter file? is it the real source of the error?
Could someone help me figuring out a solution to get the restraints to work for D3O(+), please?
Maxime
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-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov
participants (3)
-
Esko Oksanen -
Maxime Cuypers -
Nigel Moriarty