- This topic has 6 replies, 3 voices, and was last updated 9 years, 1 month ago by Anonymous.
September 21, 2014 at 12:53 am #1993Anonymous
I try to follow protocol and want to have fragment picker components for running Flexpepdock ab-initio protocol. But program return the ERROR. Can someone give me solution.
Thank alot for that.
this is my flag:
quoto_scores.wghts file is
SecondarySimilarity 350 1.0 – psipred
SecondarySimilarity 300 1.0 – sam
SecondarySimilarity 250 1.0 – porter
RamaScore 150 2.0 – psipred
RamaScore 150 2.0 – porter
RamaScore 150 2.0 – sam
ProfileScoreL1 200 2.0 –
PhiPsiSquareWell 100 0.0 –
FragmentCrmsd 30 0.0 –
ERROR AFTER RUNNING:
[node08:00924] *** Process received signal ***
[node08:00924] Signal: Segmentation fault (11)
[node08:00924] Signal code: Address not mapped (1)
[node08:00924] Failing at address: (nil)
[node08:00924] [ 0] /lib64/libpthread.so.0 [0x3a77a0ebe0]
[node08:00924] [ 1] /home/tuongvy/SW/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libprotocols_a.2.so(_ZN9protocols11frag_picker6scores23MakeSecondarySimilarity4makeEmdbN7utility7pointer10owning_ptrINS0_14FragmentPickerEEESs+0x3c) [0x2b1f50803e3c]
[node08:00924] [ 2] /home/tuongvy/SW/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libprotocols_a.2.so(_ZN9protocols11frag_picker6scores20FragmentScoreManager21create_scoring_methodERKSsmddbN7utility7pointer10owning_ptrINS0_14FragmentPickerEEESs+0x24e) [0x2b1f507fa21e]
[node08:00924] [ 3] /home/tuongvy/SW/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libprotocols_a.2.so(_ZN9protocols11frag_picker6scores20FragmentScoreManager13create_scoresERKSsN7utility7pointer10owning_ptrINS0_14FragmentPickerEEE+0x56f) [0x2b1f507fb3df]
[node08:00924] [ 4] /home/tuongvy/SW/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libprotocols_a.2.so(_ZN9protocols11frag_picker14FragmentPicker18parse_command_lineEv+0x1a54) [0x2b1f50903914]
[node08:00924] [ 5] /home/tuongvy/SW/rosetta3.4/rosetta_source/bin/fragment_picker.mpi.linuxgccrelease(main+0x145) [0x406eb5]
[node08:00924] [ 6] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3a76a1d994]
[node08:00924] [ 7] /home/tuongvy/SW/rosetta3.4/rosetta_source/bin/fragment_picker.mpi.linuxgccrelease(__gxx_personality_v0+0x191) [0x406969]
[node08:00924] *** End of error message ***
mpiexec noticed that process rank 7 with PID 924 on node node08.mark.pknu.ac.kr exited on signal 11 (Segmentation fault).
September 22, 2014 at 4:37 pm #10298Anonymous
Fragment picking needs a sequence as input, not a structure. One of “-in::file::checkpoint”, “-in::file::binary_chk”, “-in::file::pssm” or “-in::file::fasta” should be provided.
If you don’t know what to provide the other options, I’d recommend sticking with the fasta sequence option. The script “main/source/src/python/apps/public/pdb2fasta.py” is able to extract a fasta sequence from a PDB file. (You will want to examine and possibly edit the output before using, though.)
September 24, 2014 at 5:02 pm #10314Anonymous
Please download the FlexPepDock tutorial available here: http://bit.ly/NfW6tq. You can set up fragment creation using the instructions given. You need to run PSIpred and Blast locally. From our analysis, we have see that PSIpred work well enough for small peptides, though it’s not optimized for small length. You need to edit make_fragments.pl file to include the paths of the binaries and databases. We only use PSIpred predicted secondary structure and blast output to get the fragments. Then fragment_picker is used to get the fragments. All are set up in prep_abinitio.sh script. Please go though te README file. You can have a look at the scoring method used to get the fragments. Please let us know if you have any queries.
best of luck!
September 23, 2014 at 5:58 am #10307Anonymous
thank a lot for your susggestion.
I have the peptide only 7 amino acid, the sequence is so short and PsiPred webserve can not run (the error “the sequence is too short). How can I get secondary structure prediction of this peptide?
when I use http://distill.ucd.ie/porter/ to get secondary structure predition the result return like this :
But, the program can not rescogine this file.
I want to use BestFragmentProtocol
# Input databases
# Query-related input files
-frags::ss_pred input_files/2jsvX.psipred.ss2 predA
# Weights file
# What should we do?
# three-mers only, please
this protocol require psipred.ss2 file?
And another question :
With only .fasta file, Can I run fragment Picker?
Thank a lot.
September 24, 2014 at 4:36 am #10313Anonymous
the website, somtimes, have the problem such the updating can not going on?
Could you please post again your reply
September 25, 2014 at 4:52 am #10323Anonymous
I try to follow the instructions, and try to run fragment_picker locally. Some the paths of binaries and databases can not edit because I can not find (such as : robetta/databases/local_db/nr/nr_pfilt, robetta/src/shareware/sam.predict2nd …).
And another question: when I used different pdb files for reference, I got the same result fragment. it means the pdb file fragment is just for caculting RMSD and it was not effect the picking and collecting processing, right?
October 6, 2014 at 11:50 pm #10400Anonymous
Frgament picking relies on several pieces of external software, including the BLAST nr database, and things like sam, jufo, etc. You’ll need to install them locally, and then change the directory locations in the scripts to point to the locations on your machine.
Fragment picking is also primarily sequence based. So the different input structures will have little to no effect on the results of your fragment picking.
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