Mandar Kulkarni

ROOT in pdb to pdbqt conversion

2

Hi, I am converting the RNA PDB file built by Maestro to pdbqt. `ls 1KOC_clean.pdb | xargs /usr/local/bin/obabel -xcr -ipdb -opdbqt | tee receptor.pdbqt` However, this conversion prints the "ROOT"...

Flexible docking tutorial : no HD map file after autogrid4

4

Dear all, I am trying a flexible docking tutorial. I am facing a problem with the generation of the map files. I am using a file `1fpu_receptorH.pdb` from the data...

Hi, I am using Barnaba to extract backbone torsion angles PDB 5YTT (chain B) (Image and PDB file attached here). It has a missing residue, however, barnaba give values for...

Hi, I am using rna_cluster to cluster top 1% of structures after FARFAR2 run. `rna_cluster.mpi.linuxgccrelease -in:file:silent ../simple_cycle.out -out:file:silent clustered.out -nstruct 2000 -cluster:radius 5` After that structures from same cluster (confirmed...