I have 3884 PDB files generated by pd2_ca2main. PD2 CA2main is server for reconstructing the backbone of Calpha proteins using Gaussian mixture models.
All of these files have duplicate atoms or alternate coordinates.
How can I clean these PDB files using Visual Molecular Dynamics (VMD) or Scaleable Molecular Dynamics (NAMD) *?
Can anyone tell me what command I should use in console mode?
* note, this server may be unavailable