How can I clean a PDB file using VMD or NAMD?

Question

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

Answer 1

You can use Chimera for this. The following code cleans your pdb file and write new pdb file.

import chimera
from DockPrep import prep
from chimera import runCommand, openModels

models = chimera.openModels.list(modelTypes=[chimera.Molecule])
prep(models)
runCommand("write format pdb 0 molecule.pdb")

You can run the code with

 chimera --nogui file.pdb code.py