I am working on molecular dynamics simulation of a protein structure with approximately 1900 residues. In PDB, only c-alpha trace was available for this protein. I generated full-atom model using the following steps:
- C-alpha trace is downloaded from PDB
- Side-chains atoms are generated using MaxSprout
- Missing atoms added using DeepView
After these 3 steps, I assessed the quality of the structure using PROCHECK via PDBSum and noticed that approximately 3% of the residues are in the disallowed region.
I would like to know the best practice to fix the residues in disallowed region ? Is there any tool or methodology (for example energy minimization) that can adjust the phi-psi values of residues in disallowed region ? I would also like to know if there is any better equivalent for the tools that I have used for side-chain atom generation and fixing the missing atoms.
Looking forward for your suggestions.