Hi,
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?
Joanna