Hi, I ran flexpepdock with nstruct 10, however, i don't see any score.sc generated after completion.? Why is that so and how can I resolve it.? Thanks. =)
I'm not sure what monos_morpheus's solution was, but I suggest looking around the various directories you've set. Look at the directory you launched the executable from as well as any paths that you set in the command line. The scorefile might not have ended up in the directory you though it was going to end up in.
Actually, there is this other issue, which may be linked to me not getting a scores file. After prepacking, I notice that the prepacked pdb file (the one after -s above) has only a single chain, i.e., all the ATOMs simply follow each other, with only one final TER, then the pose energies table. Is that what one expects, given that the input pdb (before prepacking) is: "all protein atoms TER all ligand (it's a peptide) atoms TER"? Sorry if that's a stupid question, I haven't been using Rosetta for too long.
I think the issue is that you're using silent file output. I don't believe that you'll get a separate scorefile from a silent file - instead the data will be included in the silent file. You can get a scorefile equivalent by extracting the lines starting with "SCORE:" with grep:
egrep '^SCORE:' decoys.silent > score.sc
Regarding the TER cards, they're not always needed. For example, if the protein and the ligand are on different PDB chains (e.g. A and B) they don't need a TER between them. Only if you want (polymer) residues with the same PDB chain ID to be on different chains will you need the intervening TER record.
Solved.
May I kindly ask what the solution to this one was? I'm having the exact same problem.
Thanks a lot,
Rob
I'm not sure what monos_morpheus's solution was, but I suggest looking around the various directories you've set. Look at the directory you launched the executable from as well as any paths that you set in the command line. The scorefile might not have ended up in the directory you though it was going to end up in.
Thanks a lot. Unfortunately, no score.sc file there (have done a 'find' on all drives). Maybe there's a problem with the way I call things? See here:
PREPACK:
~/rosetta/FlexPepDocking.linuxgccdebug -database (path here) -s receptor_pdb_plus_model.pdb -flexpep_prepack -ex1 -ex2aro
RUN:
~/rosetta/FlexPepDocking.linuxgccdebug -database (path here) -s receptor_pdb_plus_model_prepacked.pdb -out:file:silent decoys.silent -out:file:silent_struct_type binary -pep_refine -ex1 -ex2aro -use_input_sc -nstruct 200 >stdout 2>stderr
Actually, there is this other issue, which may be linked to me not getting a scores file. After prepacking, I notice that the prepacked pdb file (the one after -s above) has only a single chain, i.e., all the ATOMs simply follow each other, with only one final TER, then the pose energies table. Is that what one expects, given that the input pdb (before prepacking) is: "all protein atoms TER all ligand (it's a peptide) atoms TER"? Sorry if that's a stupid question, I haven't been using Rosetta for too long.
Cheers,
Rob
I think the issue is that you're using silent file output. I don't believe that you'll get a separate scorefile from a silent file - instead the data will be included in the silent file. You can get a scorefile equivalent by extracting the lines starting with "SCORE:" with grep:
egrep '^SCORE:' decoys.silent > score.sc
Regarding the TER cards, they're not always needed. For example, if the protein and the ligand are on different PDB chains (e.g. A and B) they don't need a TER between them. Only if you want (polymer) residues with the same PDB chain ID to be on different chains will you need the intervening TER record.
Thanks! That actually helps a lot :)