jian-zhan/rna-briq

Robust RNA structure refinement by a nucleobase-centric sampling algorithm coupled with a backbone rotameric and quantum-mechanical-energy-scaled base-base knowledge-based potential

rna-briq's Issues

Broken link to http://servers.sparks-lab.org/downloads/RNA-BRiQ-data.tar.gz

Connection timed out Error code 522

Can't open file error.

Thanks for providing the code for your method. I have been trying to run the method but I keep getting can't open file error for files inside the BRiQ_data directory. Can you please point out that what might be going wrong? Here's the complete error:

abahai@odin:~/RNA-BRiQ/demo/refinement$ bash run.sh
check input file:
init energy table:
can't open file: /home/abahai/BRiQ_data/sphere2000.index
can't open file: /home/abahai/BRiQ_data/sphere2000.index_nearest3Pts
can't open file /home/abahai/BRiQ_data/split6D/n1Keys/sp2000/AA.ene
can't open file /home/abahai/BRiQ_data/split6D/n2Keys/sp2000/AA.ene
can't open file /home/abahai/BRiQ_data/split6D/n3Keys/sp2000/AA.ene
can't open file /home/abahai/BRiQ_data/split6D/n1Keys/sp2000/AU.ene
can't open file /home/abahai/BRiQ_data/split6D/n2Keys/sp2000/AU.ene
can't open file /home/abahai/BRiQ_data/split6D/n3Keys/sp2000/AU.ene
can't open file /home/abahai/BRiQ_data/split6D/n1Keys/sp2000/AG.ene
can't open file /home/abahai/BRiQ_data/split6D/n2Keys/sp2000/AG.ene
can't open file /home/abahai/BRiQ_data/split6D/n3Keys/sp2000/AG.ene
can't open file /home/abahai/BRiQ_data/split6D/n1Keys/sp2000/AC.ene
can't open file /home/abahai/BRiQ_data/split6D/n2Keys/sp2000/AC.ene
can't open file /home/abahai/BRiQ_data/split6D/n3Keys/sp2000/AC.ene
can't open file /home/abahai/BRiQ_data/split6D/n1Keys/sp2000/UA.ene
can't open file /home/abahai/BRiQ_data/split6D/n2Keys/sp2000/UA.ene
can't open file /home/abahai/BRiQ_data/split6D/n3Keys/sp2000/UA.ene
can't open file /home/abahai/BRiQ_data/split6D/n1Keys/sp2000/UU.ene
can't open file /home/abahai/BRiQ_data/split6D/n2Keys/sp2000/UU.ene
can't open file /home/abahai/BRiQ_data/split6D/n3Keys/sp2000/UU.ene
can't open file /home/abahai/BRiQ_data/split6D/n1Keys/sp2000/UG.ene
can't open file /home/abahai/BRiQ_data/split6D/n2Keys/sp2000/UG.ene
can't open file /home/abahai/BRiQ_data/split6D/n3Keys/sp2000/UG.ene
can't open file /home/abahai/BRiQ_data/split6D/n1Keys/sp2000/UC.ene
can't open file /home/abahai/BRiQ_data/split6D/n2Keys/sp2000/UC.ene
can't open file /home/abahai/BRiQ_data/split6D/n3Keys/sp2000/UC.ene
can't open file /home/abahai/BRiQ_data/split6D/n1Keys/sp2000/GA.ene
can't open file /home/abahai/BRiQ_data/split6D/n2Keys/sp2000/GA.ene
can't open file /home/abahai/BRiQ_data/split6D/n3Keys/sp2000/GA.ene
can't open file /home/abahai/BRiQ_data/split6D/n1Keys/sp2000/GU.ene
can't open file /home/abahai/BRiQ_data/split6D/n2Keys/sp2000/GU.ene
can't open file /home/abahai/BRiQ_data/split6D/n3Keys/sp2000/GU.ene
can't open file /home/abahai/BRiQ_data/split6D/n1Keys/sp2000/GG.ene
can't open file /home/abahai/BRiQ_data/split6D/n2Keys/sp2000/GG.ene
can't open file /home/abahai/BRiQ_data/split6D/n3Keys/sp2000/GG.ene
can't open file /home/abahai/BRiQ_data/split6D/n1Keys/sp2000/GC.ene
can't open file /home/abahai/BRiQ_data/split6D/n2Keys/sp2000/GC.ene
can't open file /home/abahai/BRiQ_data/split6D/n3Keys/sp2000/GC.ene
can't open file /home/abahai/BRiQ_data/split6D/n1Keys/sp2000/CA.ene
can't open file /home/abahai/BRiQ_data/split6D/n2Keys/sp2000/CA.ene
can't open file /home/abahai/BRiQ_data/split6D/n3Keys/sp2000/CA.ene
can't open file /home/abahai/BRiQ_data/split6D/n1Keys/sp2000/CU.ene
can't open file /home/abahai/BRiQ_data/split6D/n2Keys/sp2000/CU.ene
can't open file /home/abahai/BRiQ_data/split6D/n3Keys/sp2000/CU.ene
can't open file /home/abahai/BRiQ_data/split6D/n1Keys/sp2000/CG.ene
can't open file /home/abahai/BRiQ_data/split6D/n2Keys/sp2000/CG.ene
can't open file /home/abahai/BRiQ_data/split6D/n3Keys/sp2000/CG.ene
can't open file /home/abahai/BRiQ_data/split6D/n1Keys/sp2000/CC.ene
can't open file /home/abahai/BRiQ_data/split6D/n2Keys/sp2000/CC.ene
can't open file /home/abahai/BRiQ_data/split6D/n3Keys/sp2000/CC.ene
can't open file: /home/abahai/BRiQ_data/clashDistance.txt