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Bit of a complicated issue here so apologies in advance if it's not entirely clear - happy to provide clarification.

Hello all,

I have been trying to dock a library of ligands to a protein while following the Meiler lab tutorials. While I have been able to prepare most of the prerequisite files, I am unsure how I am supposed to obtain 'crystal_complex.pdb'. Trying to download the protein bound with a ligand .pdb file from the protein data bank and using that as my crystal_complex.pdb does not seem to work. While it seems that options.txt and dock.xml have been set up correctly, protein complex.pdb is the only thing preventing me from running the docking itself.

Hello!

I was a little bit confused about what exactly the stub libraries are and how we are supposed to generate them. From what I understand, they're simply just disembodied residues that we consider "important" to the interface in the docked complex. So, are the stub files just generated by taking a protein structure and deleting everything except for the hotspot residue, then saving that singular residue as a PDB file? Also, is it possible to assign hotspot residues to both chains that we are docking together?

Thank you so much.

Hi,

I want to run FARFAR2 MPI protocol to build 3D model of 70 nt long RNA with command:

mpiexec -np 8 ${rna_denovo_mpi} -fasta seq.fasta -secstruct_file rna.secstruct -minimize_rna true -cycles 20000 -nstruct 5000 -fragment_homology_rmsd 1.2 -exclusion_match_type MATCH_YR -out:file:silent $outfile_name  > out.log

I am looking for suggestion about two parts:

1. How to decide optimal value for nstruct? I understand it could depend on RNA length, is there any thumb rule to decide -nstruct option?