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Dear users,
I am having trouble to use the SOAP score. I already read the manual and tried to find tutorials online but none addressed the issues I am having.
I downloaded the SOAP-Protein potential file from the SOAP website and placed at C:\ProgramFiles\Modeller9.25\lib\x86_64-w64, uncommented the SOAP-related lines in model-single.py but when i try to run the script i receive an error:
hdf5err____E> unable to open file
Here's a description of what I get back from the code:
MODELLER 9.25, 2020/09/03, r11894
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2020 Andrej Sali
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, WinNT 10.0 build 18363, BRENDA, SMP, unknown
Date and time of compilation : 2020/09/03 08:23:39
MODELLER executable type : x86_64-w64
Job starting time (YY/MM/DD HH:MM:SS): 2020/12/04 14:09:46
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
read_to_681_> topology.submodel read from topology file: 3
The following 1 residues contain 6-membered rings with poor geometries
after transfer from templates. Rebuilding rings from internal coordinates:
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
0 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
0 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 6900 6307
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified: ARG:OXT ARG
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 81
Number of all, selected real atoms : 681 681
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 6307 6307
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 109400
Dynamic pairs routine : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 1 9999
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T
Current energy : -5509.1812
DOPE score : -5509.181152
>> Model assessment by SOAP-Protein-OD score
HDF5-DIAG: Error detected in HDF5 (1.10.5) thread 0:
#000: C:\Users\ben\Desktop\hdf5-1.10.5\src\H5F.c line 509 in H5Fopen(): unable to open file
minor: Unable to open file
#001: C:\Users\ben\Desktop\hdf5-1.10.5\src\H5Fint.c line 1498 in H5F_open(): unable to open file: time = Fri Dec 04 14:09:54 2020
, name = 'C:\Program Files\Modeller9.25/modlib\/soap_protein_od.hdf5', tent_flags = 0
minor: Unable to open file
#002: C:\Users\ben\Desktop\hdf5-1.10.5\src\H5FD.c line 734 in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
#003: C:\Users\ben\Desktop\hdf5-1.10.5\src\H5FDsec2.c line 346 in H5FD_sec2_open(): unable to open file: name = 'C:\Program Files\Modeller9.25/modlib\/soap_protein_od.hdf5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags =
0
minor: Unable to open file
hdf5err____E> unable to open file
Traceback (most recent call last):
File "c:/Users/Brenda/Documents/Doutorado/Modelagem_ProFurina/1KN6_model1/model-single.py", line 13, in <module>
File "C:\Program Files\Modeller9.25\modlib\modeller\automodel\automodel.py", line 150, in make
self.multiple_models(atmsel)
File "C:\Program Files\Modeller9.25\modlib\modeller\automodel\automodel.py", line 255, in multiple_models
self.outputs.append(self.single_model(atmsel, num))
File "C:\Program Files\Modeller9.25\modlib\modeller\automodel\automodel.py", line 352, in single_model
self.model_analysis(atmsel, filename, out, num)
File "C:\Program Files\Modeller9.25\modlib\modeller\automodel\automodel.py", line 391, in model_analysis
assess_keys = self.assess(atmsel, self.assess_methods, out)
File "C:\Program Files\Modeller9.25\modlib\modeller\automodel\automodel.py", line 515, in assess
(key,value) = method(atmsel)
File "C:\Program Files\Modeller9.25\modlib\modeller\terms.py", line 60, in __call__
return (self.name, atmsel.assess(self))
File "C:\Program Files\Modeller9.25\modlib\modeller\selection.py", line 726, in assess
molpdf, terms = assessor._assess(self, output=output, **vars)
File "C:\Program Files\Modeller9.25\modlib\modeller\terms.py", line 56, in _assess
return atmsel.energy(edat=self._get_energy_data_cached(),
File "C:\Program Files\Modeller9.25\modlib\modeller\terms.py", line 68, in _get_energy_data_cached
self._edat = self._get_energy_data_all()
File "C:\Program Files\Modeller9.25\modlib\modeller\terms.py", line 73, in _get_energy_data_all
edat.energy_terms.append(self)
File "C:\Program Files\Modeller9.25\modlib\modeller\util\modlist.py", line 154, in append
self.insert(len(self), obj)
File "C:\Program Files\Modeller9.25\modlib\modeller\util\modlist.py", line 166, in insert
File "C:\Program Files\Modeller9.25\modlib\modeller\terms.py", line 38, in _insfunc
obj._add_term(self.__edat(), indx)
File "C:\Program Files\Modeller9.25\modlib\modeller\soap_protein_od.py", line 20, in _add_term
_modeller.mod_soap_od_create(edat, indx, self._group.get_type(),
_modeller.ModellerError: hdf5err____E> unable to open file
Could someone help me with this problem?
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