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sunandanmukherjee / QRNAS

QRNAS: Quick Refinement of Nucleic Acid Structures
GNU General Public License v3.0
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QRNA -i 1l2x.pdb "Warning: empty system, cannot proceed." #5

Closed mmagnus closed 2 years ago

mmagnus commented 2 years ago 
ubuntu@ip-172-31-0-216:~/rna-tools/opt/QRNAS$ make
g++ --std=c++03 -Wall -O3 -Iinclude -DSEQUENTIAL -o QRNA bprestr.cpp main.cpp tatom.cpp tbond.cpp tdihed.cpp textutils.cpp timpro.cpp tmolecule.cpp tposrestr.cpp tvector.cpp distrestr.cpp tangle.cpp tbasepair.cpp tconsts.cpp telectr.cpp thbond.cpp tlennard.cpp tnonbond.cpp tspring.cpp
tmolecule.cpp: In static member function ‘static bool TMolecule::bCompleteResidue(std::vector<TAtom>&, std::map<std::__cxx11::basic_string<char>, int>&, std::map<std::__cxx11::basic_string<char>, TAtom>&, const string&, const string&)’:
tmolecule.cpp:1149:12: warning: variable ‘bMatch1’ set but not used [-Wunused-but-set-variable]
 1149 |       bool bMatch1 = false, bMatch2 = false, bMatch3 = false, bMatch4 = false;
      |            ^~~~~~~

then in .bashrc

QRNAS_FF_DIR=/home/ubuntu/rna-tools/opt/QRNAS/forcefield

re-run bash and cmd

QRNA -i 1l2x.pdb &> filename.log

-----------------------------------------------------------------------------
Warning: More threads than cores available.
Parameters to be used:
Number of minimization steps (NSTEPS): 100000
Golden section step sizes: maximal (MAXSTEP): 0.0001
                           minimal (MINSTEP): 1e-08
Verbosity (VERBOSE): 1
Write output every: 100 steps (WRITEFREQ)
Record trajectory (TRAJECTORY): disabled
Pedantic treatment of molecules (PEDANTICMOL): disabled
Van der Waals cutoff radius (CUTOFF): 12
Born generalized solvent (USEBORN): disabled
Constraints on secondary struct. (SSCONSTR): enabled
Auto-detection of secondary struct. (SSDETECT): enabled
Secondary structure (SECSTRUCT): none specified
Hydrogen bonds (HBONDS): enabled
Electrostatics (ELECTR): enabled
van der Waals interactions (VANDERWAALS): enabled
Anti-blow-up protection (BLOWGUARD): enabled
Occupancy as positional restraint (POSRESTRAINTS): disabled
Restraints description (RESTRFILE): none
Number of parallel threads: 4

-----------------------------------------------------------------------------
Internal Warning: unknown atom type(s) in bond: C2 H5
Internal Warning: unknown atom type(s) in bond: C2 N*
Internal Warning: unknown atom type(s) in bond: C2 NB
Internal Warning: unknown atom type(s) in bond: C C1
Internal Warning: unknown atom type(s) in bond: CA C1
Internal Warning: unknown atom type(s) in bond: C1 C1
Internal Warning: unknown atom type(s) in bond: C1 CT
Internal Warning: unknown atom type(s) in bond: C1 HA
Internal Warning: unknown atom type(s) in bond: C1 H4
Internal Warning: unknown atom type(s) in bond: C1 N*
Internal Warning: unknown atoms in angle: H5 C2 N*
Internal Warning: unknown atoms in angle: H5 C2 NB
Internal Warning: unknown atoms in angle: N* C2 NB
Internal Warning: unknown atoms in angle: CB N* C2
Internal Warning: unknown atoms in angle: C2 N* CT
Internal Warning: unknown atoms in angle: CB NB C2
Internal Warning: unknown atoms in angle: C1 C NA
Internal Warning: unknown atoms in angle: C1 C O
Internal Warning: unknown atoms in angle: C1 CA N2
Internal Warning: unknown atoms in angle: C1 CA NC
Internal Warning: unknown atoms in angle: C C1 C1
Internal Warning: unknown atoms in angle: C C1 CT
Internal Warning: unknown atoms in angle: C C1 HA
Internal Warning: unknown atoms in angle: C C1 H4
Internal Warning: unknown atoms in angle: CA C1 C1
Internal Warning: unknown atoms in angle: CA C1 HA
Internal Warning: unknown atoms in angle: CA C1 H4
Internal Warning: unknown atoms in angle: C1 C1 CT
Internal Warning: unknown atoms in angle: C1 C1 HA
Internal Warning: unknown atoms in angle: C1 C1 H4
Internal Warning: unknown atoms in angle: C1 C1 N*
Internal Warning: unknown atoms in angle: H4 C1 N*
Internal Warning: unknown atoms in angle: H1 CT C1
Internal Warning: unknown atoms in angle: HC CT C1
Internal Warning: unknown atoms in angle: C N* C1
Internal Warning: unknown atoms in angle: C1 N* CT
Internal Warning: unknown atom(s) in dihedral: X C2 N* X
Internal Warning: unknown atom(s) in dihedral: X C2 NB X
Internal Warning: unknown atom(s) in dihedral: X C C1 X
Internal Warning: unknown atom(s) in dihedral: X CA C1 X
Internal Warning: unknown atom(s) in dihedral: X C1 C1 X
Internal Warning: unknown atom(s) in dihedral: X C1 CT X
Internal Warning: unknown atom(s) in dihedral: X C1 N* X
Internal Warning: unknown atom(s) in dihedral: HC CT C1 C1
Internal Warning: unknown atom(s) in dihedral: HC CT C1 C1
Internal Warning: unknown atom(s) in dihedral: C1 C1 C O
Internal Warning: unknown atom(s) in dihedral: C1 C1 C O
Internal Warning: unknown atom(s) in dihedral: OS CT N* C2
Internal Warning: unknown atom(s) in dihedral: OS CT N* C2
Internal Warning: unknown atom(s) in dihedral: OS CT N* C2
Internal Warning: unknown atom(s) in dihedral: OS CT N* C1
Internal Warning: unknown atom(s) in dihedral: OS CT N* C1
Internal Warning: unknown atom(s) in dihedral: OS CT N* C1
Internal Warning: unknown atom(s) in dihedral: OS CT N* C1
Internal Warning: unknown atom(s) in improper: C C1 N* CT
Internal Warning: unknown atom(s) in improper: C C1 C1 CT
Internal Warning: unknown atom(s) in improper: C1 N2 CA NC
Initializing...
Generic atom descriptions read:     47
Generic bond descriptions read:     199
Generic angle descriptions read:    567
Generic dihedral descriptions read: 812
Generic improper descriptions read: 116
Generic vdW descriptions read:      47
-----------------------------------------------------------------------------
=============================================================================
Reading PDB file: 1l2x.pdb
=============================================================================
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue: GTP
Error: unknown residue(s). Molecule discarded.
Error: unknown residue: MG
Error: unknown residue: MG
Error: unknown residue: MG
Error: unknown residue: MG
Error: unknown residue: MG
Error: unknown residue: MG
Error: unknown residue: NA
Error: unknown residue: NA
Error: unknown residue: NA
Error: unknown residue: K
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue: HOH
Error: unknown residue(s). Molecule discarded.
-----------------------------------------------------------------------------
Building interresidual nonbonded pairs & H-bonds (it may take a while)...
Number of electrostatic pairs:   0
Number of van der Waals pairs:   0
Number of H-bonds built:         0
Number of spring restraints:     0
Number of positional restraints: 0
Number of base pairs built:      0
Number of molecules (chains) read: 0
-----------------------------------------------------------------------------
Warning: empty system, cannot proceed.
nithinaneesh commented 2 years ago

Use a clean version of the PDB file:

grep '^ATOM' 1l2x.pdb >1l2x_1.pdb
QRNA -i 1l2x_1.pdb

This should work :-)

mmagnus commented 2 years ago

Awsome! Works! Thank you @nithinaneesh !

│ orming minimization step: 860. Total energy = 2410.1449 kcal/mol (2406.3849 without restraints)                                                         │
│ orming minimization step: 861. Total energy = 2407.8991 kcal/mol (2404.1404 without restraints)                                                         │
│ orming minimization step: 862. Total energy = 2405.6567 kcal/mol (2401.8992 without restraints)                                                         │
│ orming minimization step: 863. Total energy = 2403.4175 kcal/mol (2399.6613 without restraints)                                                         │
│ orming minimization step: 864. Total energy = 2401.1816 kcal/mol (2397.4268 without restraints)