SimRNAweb


SimRNA (tetraloop)

RNA models for: 4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4 (tetraloop)

CGCGCAAGCG
(((....)))
magnus@genesilico.pl
tetraloop_clean_ox.pdb  frozen: A:4-7
n steps: 100 (~ n of SimRNA frames: 8000, curr n of frames 8081 = 101.0%)

The representatives of top three clusters of your simulation:

The trafl file for the simulation can be found here (the file might be > 1GB!).

The raw output files for each step of the pipeline can be found here

#1 cluster (final prediction):

4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4

The secondary structures of the representatives of top three clusters.

CGCGCAAGCG

> 4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_ALL_thrs1.00A_clust01-000001.ss_detected
(((....)))

The log of the data processing.

Processing log:
2016-03-31 00:25
WORKING_DIR /home/magnus/SimRNA_automation/WORKING_SPACE
FRACTION_LOWEST_ENERGY_FRAMES_TO_CLUSTER: 0.01
number of run directories detected: 8
making directory: /home/magnus/SimRNA_automation/WORKING_SPACE/4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4/processing_results
requested subdirectory: processing_results already exists .. removing the directory!!!!!
being in /home/magnus/SimRNA_automation/WORKING_SPACE/4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4/processing_results  running command:
cat ../run_??/*.trafl > 4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_ALL.trafl
nframes: 8081
clustering ... assuming:
--- fraction of lowest energy frames to clustering: 0.01
--- rmsd thrs for clustering 0.1*seq_lenght which is: 1.0
../../../bin/clustering 4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_ALL.trafl 0.01 1.0 > clustering.log 2>&1
number of clusters to process: 1
extracting pdbs, reconstructing all atom representation
creating symlink 'data'
../../../bin/SimRNA_trafl2pdbs ../run_01/4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_01_01-000001.pdb 4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_ALL_thrs1.00A_clust01.trafl 1 AA > 4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_ALL_thrs1.00A_clust01.log 2>&1
making directory: output_PDBS
directory already exists
detected pdb files in: processing_results:
curr_pdb_name 4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_ALL_thrs1.00A_clust01-000001.pdb
curr_pdb_name 4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_ALL_thrs1.00A_clust01-000001_AA.pdb
copying pdb and ss_detected files to: output_PDBS just to store them there
DONE :-)
Job log:
SimRNA_automatation
--------------------------------------------------------------------------------
2016-03-31 00:17
usage: run_SimRNA_prediction.py job_id_name file_sequence [file_second_strc] [pdb_file] [restraints_file] [nsteps] [debug true|false]
note: job_id_name should be legal string, to be used to set up working directory for this job
note: file_sequence and (optional) file_second_strc has to comply SimRNA requirements for those files
WORKING_DIR: /home/magnus/SimRNA_automation/WORKING_SPACE

in /home/magnus/SimRNA_automation/WORKING_SPACE making subdirectory: 4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4


COPYING...
copying sequence file: /home/magnus/simrnaweb/media/jobs//4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4/seq.fa to: /home/magnus/SimRNA_automation/WORKING_SPACE/4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4, just to have it there (for further checking)
copying secondary structure file: /home/magnus/simrnaweb/media/jobs//4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4/seq.ss to: /home/magnus/SimRNA_automation/WORKING_SPACE/4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4, just to have it there (for further checking)
copying pdb file file: /home/magnus/simrnaweb/media/jobs//4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4/tetraloop_clean_ox.pdb to: /home/magnus/SimRNA_automation/WORKING_SPACE/4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4, just to have it there (for further checking)
copying config.dat to 4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4 to have it there, because parent one can be changed
in /home/magnus/SimRNA_automation/WORKING_SPACE/4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4 making directories:
run_01
creating symlink 'data'
making SimRNA run file: r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_01

 SimRNA (c) 2009-2015 Genesilico, ver. 3.21

 program compiled as SimRNA3: 3 atoms per base

.reading parameteres
class RNAStructure: SimRNA3 flag is set
chain 1 read from: ../seq.fa: CGCGCAAGCG
chains:
chain A contains 10 nucleotides
loading histrogram: ./data/dist_PC.data.new_hist   assigned_name: dist_PC.data.new_hist  DONE
loading histrogram: ./data/dist_CP.data.new_hist   assigned_name: dist_CP.data.new_hist  DONE
loading histrogram: ./data/angle_PCP.data.new_hist   assigned_name: angle_PCP.data.new_hist  DONE
loading histrogram: ./data/angle_CPC.data.new_hist   assigned_name: angle_CPC.data.new_hist  DONE
loading histrogram: ./data/eta_theta.data.new_hist   assigned_name: eta_theta.data.new_hist  DONE
reading conformers file: ./data/A_conformers
n_lines: 4766
   16    15    69    34    27 
   46    26   156    83    35 
   93   127  1269    89    50 
  187   157  1927    88    75 
   51    22    67    25    32 
DONE
reading conformers file: ./data/C_conformers
n_lines: 5164
    7     8    61    17     4 
   14    12   143    49    12 
   23   140  2110    21    24 
   88   101  2101    19    36 
   25    21   108     8    12 
DONE
reading conformers file: ./data/G_conformers
n_lines: 6375
   11     7    79    21    50 
   20    17   175    54    39 
   42   102  2774    90    34 
   61    94  2314    71   100 
   20    22   142    15    21 
DONE
reading conformers file: ./data/U_conformers
n_lines: 3617
    6     6    43    33    24 
   20    20   131    50    28 
   30    58  1412    30    24 
   64    82  1197    31    32 
   71    36   132    13    44 
DONE
loading histrogram: ./data/AA3.hist   assigned_name: AA3.hist  DONE
loading histrogram: ./data/AC3.hist   assigned_name: AC3.hist  DONE
loading histrogram: ./data/AG3.hist   assigned_name: AG3.hist  DONE
loading histrogram: ./data/AU3.hist   assigned_name: AU3.hist  DONE
loading histrogram: ./data/CA3.hist   assigned_name: CA3.hist  DONE
loading histrogram: ./data/CC3.hist   assigned_name: CC3.hist  DONE
loading histrogram: ./data/CG3.hist   assigned_name: CG3.hist  DONE
loading histrogram: ./data/CU3.hist   assigned_name: CU3.hist  DONE
loading histrogram: ./data/GA3.hist   assigned_name: GA3.hist  DONE
loading histrogram: ./data/GC3.hist   assigned_name: GC3.hist  DONE
loading histrogram: ./data/GG3.hist   assigned_name: GG3.hist  DONE
loading histrogram: ./data/GU3.hist   assigned_name: GU3.hist  DONE
loading histrogram: ./data/UA3.hist   assigned_name: UA3.hist  DONE
loading histrogram: ./data/UC3.hist   assigned_name: UC3.hist  DONE
loading histrogram: ./data/UG3.hist   assigned_name: UG3.hist  DONE
loading histrogram: ./data/UU3.hist   assigned_name: UU3.hist  DONE
loading histrogram: ./data/A-C4_3.hist   assigned_name: A-C4_3.hist  DONE
loading histrogram: ./data/C-C4_3.hist   assigned_name: C-C4_3.hist  DONE
loading histrogram: ./data/G-C4_3.hist   assigned_name: G-C4_3.hist  DONE
loading histrogram: ./data/U-C4_3.hist   assigned_name: U-C4_3.hist  DONE
loading histrogram: ./data/A-P_3.hist   assigned_name: A-P_3.hist  DONE
loading histrogram: ./data/C-P_3.hist   assigned_name: C-P_3.hist  DONE
loading histrogram: ./data/G-P_3.hist   assigned_name: G-P_3.hist  DONE
loading histrogram: ./data/U-P_3.hist   assigned_name: U-P_3.hist  DONE
loading histrogram: ./data/A_3_exvol.hist   assigned_name: A_3_exvol.hist  DONE
scaling: histogram A_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/C_3_exvol.hist   assigned_name: C_3_exvol.hist  DONE
scaling: histogram C_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/G_3_exvol.hist   assigned_name: G_3_exvol.hist  DONE
scaling: histogram G_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/U_3_exvol.hist   assigned_name: U_3_exvol.hist  DONE
scaling: histogram U_3_exvol.hist was multiplied by 0.100000
scaling: histogram eta_theta.data.new_hist was multiplied by 0.400000
eta-theta term was reweighted by factor 0.400000 provided by the user

random seed = 1
number of iterations = 1
trajectory write in every 16000 iterations
initTemp  = 1.350
finalTemp = 0.900
tempStep = -4.500000e-01
DONE

.calculating
==================================
Write number: 1

Temperature: 1.350000

Total energy of system -33.287999
where:
	Base-Base interactions energy    0.000
	where:  short stacking energy    0.000 

	Base-Backbone interact. energy   -0.000

	Local geometry energy -33.287907
	where:
		bonds (distance)  C4'-P  energy:   -9.716
		bonds (distance)  P-C4'  energy:   -8.947
		flat angles   C4'-P-C4'  energy:   -6.608
		flat angles    P-C4'-P   energy:   -8.399
		tors. eta vs tors. theta energy:    0.381


.writing output

current chain energy: -31.461133
recalc. chain energy: -31.461133
numberOfNucleotides: 10
initial temperature kT: 1.350000
moves confirmed at first:  2
moves confirmed later: 3
all moves confirmed: 5
percent of confirmed moves: 5.000000

 Time of doing 1 iterations:  0.001 seconds

4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_01_*00001.pdb
['4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_01_167937-000001.pdb']
/home/magnus/SimRNA_automation/WORKING_SPACE/4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4/run_01
../../../bin/SimRNA_trafl2pdbs 4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_01_167937-000001.pdb 4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_01_167937.trafl : AA 
class RNAStructure: SimRNA3 flag is set

reading input pdb file: 4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_01_167937-000001.pdb
number of recognized chains: 1
number of read nucleotides: 10
number of read atoms: 50
chains:
chain A contains 10 nucleotides
(in case of error messages nucleotide numbering starts from 1)
loading histrogram: ./data/dist_PC.data.new_hist   assigned_name: dist_PC.data.new_hist  DONE
loading histrogram: ./data/dist_CP.data.new_hist   assigned_name: dist_CP.data.new_hist  DONE
loading histrogram: ./data/angle_PCP.data.new_hist   assigned_name: angle_PCP.data.new_hist  DONE
loading histrogram: ./data/angle_CPC.data.new_hist   assigned_name: angle_CPC.data.new_hist  DONE
loading histrogram: ./data/eta_theta.data.new_hist   assigned_name: eta_theta.data.new_hist  DONE
reading conformers file: ./data/A_conformers
n_lines: 4766
   16    15    69    34    27 
   46    26   156    83    35 
   93   127  1269    89    50 
  187   157  1927    88    75 
   51    22    67    25    32 
DONE
reading conformers file: ./data/C_conformers
n_lines: 5164
    7     8    61    17     4 
   14    12   143    49    12 
   23   140  2110    21    24 
   88   101  2101    19    36 
   25    21   108     8    12 
DONE
reading conformers file: ./data/G_conformers
n_lines: 6375
   11     7    79    21    50 
   20    17   175    54    39 
   42   102  2774    90    34 
   61    94  2314    71   100 
   20    22   142    15    21 
DONE
reading conformers file: ./data/U_conformers
n_lines: 3617
    6     6    43    33    24 
   20    20   131    50    28 
   30    58  1412    30    24 
   64    82  1197    31    32 
   71    36   132    13    44 
DONE
loading histrogram: ./data/AA3.hist   assigned_name: AA3.hist  DONE
loading histrogram: ./data/AC3.hist   assigned_name: AC3.hist  DONE
loading histrogram: ./data/AG3.hist   assigned_name: AG3.hist  DONE
loading histrogram: ./data/AU3.hist   assigned_name: AU3.hist  DONE
loading histrogram: ./data/CA3.hist   assigned_name: CA3.hist  DONE
loading histrogram: ./data/CC3.hist   assigned_name: CC3.hist  DONE
loading histrogram: ./data/CG3.hist   assigned_name: CG3.hist  DONE
loading histrogram: ./data/CU3.hist   assigned_name: CU3.hist  DONE
loading histrogram: ./data/GA3.hist   assigned_name: GA3.hist  DONE
loading histrogram: ./data/GC3.hist   assigned_name: GC3.hist  DONE
loading histrogram: ./data/GG3.hist   assigned_name: GG3.hist  DONE
loading histrogram: ./data/GU3.hist   assigned_name: GU3.hist  DONE
loading histrogram: ./data/UA3.hist   assigned_name: UA3.hist  DONE
loading histrogram: ./data/UC3.hist   assigned_name: UC3.hist  DONE
loading histrogram: ./data/UG3.hist   assigned_name: UG3.hist  DONE
loading histrogram: ./data/UU3.hist   assigned_name: UU3.hist  DONE
loading histrogram: ./data/A-C4_3.hist   assigned_name: A-C4_3.hist  DONE
loading histrogram: ./data/C-C4_3.hist   assigned_name: C-C4_3.hist  DONE
loading histrogram: ./data/G-C4_3.hist   assigned_name: G-C4_3.hist  DONE
loading histrogram: ./data/U-C4_3.hist   assigned_name: U-C4_3.hist  DONE
loading histrogram: ./data/A-P_3.hist   assigned_name: A-P_3.hist  DONE
loading histrogram: ./data/C-P_3.hist   assigned_name: C-P_3.hist  DONE
loading histrogram: ./data/G-P_3.hist   assigned_name: G-P_3.hist  DONE
loading histrogram: ./data/U-P_3.hist   assigned_name: U-P_3.hist  DONE
loading histrogram: ./data/A_3_exvol.hist   assigned_name: A_3_exvol.hist  DONE
scaling: histogram A_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/C_3_exvol.hist   assigned_name: C_3_exvol.hist  DONE
scaling: histogram C_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/G_3_exvol.hist   assigned_name: G_3_exvol.hist  DONE
scaling: histogram G_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/U_3_exvol.hist   assigned_name: U_3_exvol.hist  DONE
scaling: histogram U_3_exvol.hist was multiplied by 0.100000
DONE
reading frames from file 4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_01_167937.trafl

DONE
1 frame(s) were read
converting range: 1 1
all atom reconstruction flag is set
all atom reconstruction is ordered, reading backbone conformations:
reading conformers file: ./data/backbone_conformers
n_lines: 19919
    4     9     4    12    81    21     8    26    45    20 
   10    17     9    11    97    53    44    27    25    15 
   21    15    13    15   121   131    77    44    40    31 
   21    43    25    22   186   167    77    38    24    19 
   22    88    65    54   544   297    81    38    25    23 
   39    38    57   251  6244   479    79    32    32    52 
  232   103    79   240  6253   674    90    71   116    65 
   28    37    49    65   430   182    29    19    27    35 
   42    56    48    35    61   174    22    15    26    34 
   58    11     9     9   172    42     9    15    18    31 
DONE
reading conformers file: ./data/A_baseCoords_selfLC
n_lines: 1
    1 
DONE
reading conformers file: ./data/C_baseCoords_selfLC
n_lines: 1
    1 
DONE
reading conformers file: ./data/G_baseCoords_selfLC
n_lines: 1
    1 
DONE
reading conformers file: ./data/U_baseCoords_selfLC
n_lines: 1
    1 
DONE
Full atom reconstruction:
.

DONE
aa_fn ['4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_01_167937-000001_AA.pdb']
PDB_FILENAME_curr /home/magnus/SimRNA_automation/WORKING_SPACE/4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4/tetraloop_clean_ox.pdb
fragments in pdb A:4,5,6,7
A:4,5,6,7
['A', '4', '5', '6', '7']
ring <Structure id=ring>
chain A
4   G   G  ...coping
5   C   C  ...coping
6   A   A  ...coping
7   A   A  ...coping
Save as  /home/magnus/SimRNA_automation/WORKING_SPACE/4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4/tetraloop_clean_ox.pdb
SimRNA::test#2 -n 1 if setup is correct
cmd test:
../../../bin/SimRNA -c ../config.dat -R 1 -o 4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_01 -E 10  -S ../seq.ss  -P ../tetraloop_clean_ox.pdb  -n 1 -E 1 
SimRNA (c) 2009-2015 Genesilico, ver. 3.21

 program compiled as SimRNA3: 3 atoms per base

.reading parameteres
class RNAStructure: SimRNA3 flag is set

reading input pdb file: ../tetraloop_clean_ox.pdb
number of recognized chains: 1
number of read nucleotides: 10
number of read atoms: 216
chains:
chain A contains 10 nucleotides
(in case of error messages nucleotide numbering starts from 1)
atom position constraints swiched ON
bacause base:   G, 4 is fixed, fixing also its C4' atom
bacause base:   C, 5 is fixed, fixing also its C4' atom
bacause base:   A, 6 is fixed, fixing also its C4' atom
bacause base:   A, 7 is fixed, fixing also its C4' atom
loading histrogram: ./data/dist_PC.data.new_hist   assigned_name: dist_PC.data.new_hist  DONE
loading histrogram: ./data/dist_CP.data.new_hist   assigned_name: dist_CP.data.new_hist  DONE
loading histrogram: ./data/angle_PCP.data.new_hist   assigned_name: angle_PCP.data.new_hist  DONE
loading histrogram: ./data/angle_CPC.data.new_hist   assigned_name: angle_CPC.data.new_hist  DONE
loading histrogram: ./data/eta_theta.data.new_hist   assigned_name: eta_theta.data.new_hist  DONE
reading conformers file: ./data/A_conformers
n_lines: 4766
   16    15    69    34    27 
   46    26   156    83    35 
   93   127  1269    89    50 
  187   157  1927    88    75 
   51    22    67    25    32 
DONE
reading conformers file: ./data/C_conformers
n_lines: 5164
    7     8    61    17     4 
   14    12   143    49    12 
   23   140  2110    21    24 
   88   101  2101    19    36 
   25    21   108     8    12 
DONE
reading conformers file: ./data/G_conformers
n_lines: 6375
   11     7    79    21    50 
   20    17   175    54    39 
   42   102  2774    90    34 
   61    94  2314    71   100 
   20    22   142    15    21 
DONE
reading conformers file: ./data/U_conformers
n_lines: 3617
    6     6    43    33    24 
   20    20   131    50    28 
   30    58  1412    30    24 
   64    82  1197    31    32 
   71    36   132    13    44 
DONE
loading histrogram: ./data/AA3.hist   assigned_name: AA3.hist  DONE
loading histrogram: ./data/AC3.hist   assigned_name: AC3.hist  DONE
loading histrogram: ./data/AG3.hist   assigned_name: AG3.hist  DONE
loading histrogram: ./data/AU3.hist   assigned_name: AU3.hist  DONE
loading histrogram: ./data/CA3.hist   assigned_name: CA3.hist  DONE
loading histrogram: ./data/CC3.hist   assigned_name: CC3.hist  DONE
loading histrogram: ./data/CG3.hist   assigned_name: CG3.hist  DONE
loading histrogram: ./data/CU3.hist   assigned_name: CU3.hist  DONE
loading histrogram: ./data/GA3.hist   assigned_name: GA3.hist  DONE
loading histrogram: ./data/GC3.hist   assigned_name: GC3.hist  DONE
loading histrogram: ./data/GG3.hist   assigned_name: GG3.hist  DONE
loading histrogram: ./data/GU3.hist   assigned_name: GU3.hist  DONE
loading histrogram: ./data/UA3.hist   assigned_name: UA3.hist  DONE
loading histrogram: ./data/UC3.hist   assigned_name: UC3.hist  DONE
loading histrogram: ./data/UG3.hist   assigned_name: UG3.hist  DONE
loading histrogram: ./data/UU3.hist   assigned_name: UU3.hist  DONE
loading histrogram: ./data/A-C4_3.hist   assigned_name: A-C4_3.hist  DONE
loading histrogram: ./data/C-C4_3.hist   assigned_name: C-C4_3.hist  DONE
loading histrogram: ./data/G-C4_3.hist   assigned_name: G-C4_3.hist  DONE
loading histrogram: ./data/U-C4_3.hist   assigned_name: U-C4_3.hist  DONE
loading histrogram: ./data/A-P_3.hist   assigned_name: A-P_3.hist  DONE
loading histrogram: ./data/C-P_3.hist   assigned_name: C-P_3.hist  DONE
loading histrogram: ./data/G-P_3.hist   assigned_name: G-P_3.hist  DONE
loading histrogram: ./data/U-P_3.hist   assigned_name: U-P_3.hist  DONE
loading histrogram: ./data/A_3_exvol.hist   assigned_name: A_3_exvol.hist  DONE
scaling: histogram A_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/C_3_exvol.hist   assigned_name: C_3_exvol.hist  DONE
scaling: histogram C_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/G_3_exvol.hist   assigned_name: G_3_exvol.hist  DONE
scaling: histogram G_3_exvol.hist was multiplied by 0.100000
loading histrogram: ./data/U_3_exvol.hist   assigned_name: U_3_exvol.hist  DONE
scaling: histogram U_3_exvol.hist was multiplied by 0.100000
DONE
scaling: histogram eta_theta.data.new_hist was multiplied by 0.400000
eta-theta term was reweighted by factor 0.400000 provided by the user
begin: void RNAStructureWithRestraints::initSecondStrcRestraints(const char* path)
RNAStructureWithRestraints::secondStrcWeight = 1.000000
chain: 1: _(((....)))_
nucl1: 2, chain1: 0, <--->  nucl2: 7, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 2, chainIndex_2: 0, nuclIndex_2: 7
nucl1: 1, chain1: 0, <--->  nucl2: 8, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 1, chainIndex_2: 0, nuclIndex_2: 8
nucl1: 0, chain1: 0, <--->  nucl2: 9, chain2: 0
secondary structure restraint added:
chainIndex_1: 0, nuclIndex_1: 0, chainIndex_2: 0, nuclIndex_2: 9
 end: void RNAStructureWithRestraints::initSecondStrcRestraints(const char* path)
---------SecondStrcRestraint----------
first  atom: chain: A, nucl:   1
second atom: chain: A, nucl:  10
current score: 5.939
--------------------------------------
---------SecondStrcRestraint----------
first  atom: chain: A, nucl:   2
second atom: chain: A, nucl:   9
current score: 13.488
--------------------------------------
---------SecondStrcRestraint----------
first  atom: chain: A, nucl:   3
second atom: chain: A, nucl:   8
current score: 15.130
--------------------------------------

random seed = 1
number of iterations = 1
trajectory write in every 16000 iterations
initTemp  = 1.350
finalTemp = 0.900
tempStep = -4.500000e-01
DONE

.calculating
==================================
Write number: 1

Temperature: 1.350000

Total energy of system 138.854277
where:
	Base-Base interactions energy   -7.790
	where:  short stacking energy   -4.855 

	Base-Backbone interact. energy   11.435

	Local geometry energy 100.652989
	where:
		bonds (distance)  C4'-P  energy:  104.980
		bonds (distance)  P-C4'  energy:   -8.933
		flat angles   C4'-P-C4'  energy:    2.302
		flat angles    P-C4'-P   energy:   -1.920
		tors. eta vs tors. theta energy:    4.224
	dist. restrs. and SS energy:   34.556


.writing output

current chain energy: 137.584422
recalc. chain energy: 137.584422
---------SecondStrcRestraint----------
first  atom: chain: A, nucl:   1
second atom: chain: A, nucl:  10
current score: 5.794
--------------------------------------
---------SecondStrcRestraint----------
first  atom: chain: A, nucl:   2
second atom: chain: A, nucl:   9
current score: 13.488
--------------------------------------
---------SecondStrcRestraint----------
first  atom: chain: A, nucl:   3
second atom: chain: A, nucl:   8
current score: 14.978
--------------------------------------
numberOfNucleotides: 10
initial temperature kT: 1.350000
moves confirmed at first:  2
moves confirmed later: 1
all moves confirmed: 3
percent of confirmed moves: 3.000000

 Time of doing 1 iterations:  0.000 seconds
It seems that the setup is correct
Cmd:
../../../bin/SimRNA -c ../config.dat -R 1 -o 4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_01 -E 10  -S ../seq.ss  -P ../tetraloop_clean_ox.pdb  -n 1600000  >& r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_01.out
run_02
creating symlink 'data'
making SimRNA run file: r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_02
Cmd:
../../../bin/SimRNA -c ../config.dat -R 2 -o 4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_02 -E 10  -S ../seq.ss  -P ../tetraloop_clean_ox.pdb  -n 1600000  >& r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_02.oqsub: /usr/bin/qsub /usr/share/man/man1/qsub.1B.gz
qsub: /usr/bin/qsub /usr/share/man/man1/qsub.1B.gz
qsub: /usr/bin/qsub /usr/share/man/man1/qsub.1B.gz
qsub: /usr/bin/qsub /usr/share/man/man1/qsub.1B.gz
qsub: /usr/bin/qsub /usr/share/man/man1/qsub.1B.gz
qsub: /usr/bin/qsub /usr/share/man/man1/qsub.1B.gz
qsub: /usr/bin/qsub /usr/share/man/man1/qsub.1B.gz
ut
run_03
creating symlink 'data'
making SimRNA run file: r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_03
Cmd:
../../../bin/SimRNA -c ../config.dat -R 3 -o 4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_03 -E 10  -S ../seq.ss  -P ../tetraloop_clean_ox.pdb  -n 1600000  >& r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_03.out
run_04
creating symlink 'data'
making SimRNA run file: r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_04
Cmd:
../../../bin/SimRNA -c ../config.dat -R 4 -o 4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_04 -E 10  -S ../seq.ss  -P ../tetraloop_clean_ox.pdb  -n 1600000  >& r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_04.out
run_05
creating symlink 'data'
making SimRNA run file: r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_05
Cmd:
../../../bin/SimRNA -c ../config.dat -R 5 -o 4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_05 -E 10  -S ../seq.ss  -P ../tetraloop_clean_ox.pdb  -n 1600000  >& r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_05.out
run_06
creating symlink 'data'
making SimRNA run file: r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_06
Cmd:
../../../bin/SimRNA -c ../config.dat -R 6 -o 4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_06 -E 10  -S ../seq.ss  -P ../tetraloop_clean_ox.pdb  -n 1600000  >& r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_06.out
run_07
creating symlink 'data'
making SimRNA run file: r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_07
Cmd:
../../../bin/SimRNA -c ../config.dat -R 7 -o 4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_07 -E 10  -S ../seq.ss  -P ../tetraloop_clean_ox.pdb  -n 1600000  >& r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_07.out
run_08
creating symlink 'data'
making SimRNA run file: r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_08
Cmd:
../../../bin/SimRNA -c ../config.dat -R 8 -o 4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_08 -E 10  -S ../seq.ss  -P ../tetraloop_clean_ox.pdb  -n 1600000  >& r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_08.out
--------------------------------------------------------------------------------
SUBMITTING JOBS:
curr path /home/magnus/SimRNA_automation/WORKING_SPACE/4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4/run_01
cmd @ cluster /home/oge/bin/lx24-amd64/qsub -cwd -l h_vmem=300M -l mem_free=500M -pe mpi 10 r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_01
Your job 4414653 ("r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_01") has been submitted
curr path /home/magnus/SimRNA_automation/WORKING_SPACE/4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4/run_02
cmd @ cluster /home/oge/bin/lx24-amd64/qsub -cwd -l h_vmem=300M -l mem_free=500M -pe mpi 10 r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_02
Your job 4414654 ("r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_02") has been submitted
curr path /home/magnus/SimRNA_automation/WORKING_SPACE/4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4/run_03
cmd @ cluster /home/oge/bin/lx24-amd64/qsub -cwd -l h_vmem=300M -l mem_free=500M -pe mpi 10 r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_03
Your job 4414655 ("r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_03") has been submitted
curr path /home/magnus/SimRNA_automation/WORKING_SPACE/4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4/run_04
cmd @ cluster /home/oge/bin/lx24-amd64/qsub -cwd -l h_vmem=300M -l mem_free=500M -pe mpi 10 r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_04
Your job 4414656 ("r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_04") has been submitted
curr path /home/magnus/SimRNA_automation/WORKING_SPACE/4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4/run_05
cmd @ cluster /home/oge/bin/lx24-amd64/qsub -cwd -l h_vmem=300M -l mem_free=500M -pe mpi 10 r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_05
Your job 4414657 ("r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_05") has been submitted
curr path /home/magnus/SimRNA_automation/WORKING_SPACE/4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4/run_06
cmd @ cluster /home/oge/bin/lx24-amd64/qsub -cwd -l h_vmem=300M -l mem_free=500M -pe mpi 10 r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_06
Your job 4414658 ("r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_06") has been submitted
curr path /home/magnus/SimRNA_automation/WORKING_SPACE/4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4/run_07
cmd @ cluster /home/oge/bin/lx24-amd64/qsub -cwd -l h_vmem=300M -l mem_free=500M -pe mpi 10 qsub: /usr/bin/qsub /usr/share/man/man1/qsub.1B.gz
r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_07
Your job 4414659 ("r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_07") has been submitted
curr path /home/magnus/SimRNA_automation/WORKING_SPACE/4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4/run_08
cmd @ cluster /home/oge/bin/lx24-amd64/qsub -cwd -l h_vmem=300M -l mem_free=500M -pe mpi 10 r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_08
Your job 4414660 ("r_4371aff4-cea1-4deb-88ce-fbb9dc6ae5a4_run_08") has been submitted
run_SimRNA_prediction .. [OK]