I have a dcd trajectory made by VMD (originally this traj was made with AMBER) and initial pdb file for this trajectory. I want to calculate some energies from this trajectory in charmm. However when I make the psf from the initial pdb, the atom order is different than in the pdb (in fact it is the same as in charmm topology) and as a consequence, when I read the trajectory, the coordinated do not correspond to the correct atoms.
It is possible to make the psf with exactly the same atom order as in the initial pdb?