Analyzing a Charmm/NAMD generated trajectory in Amber

To convert a Charmm DCD trajectory into an Amber trajectory that can be interpreted fully with the Amber suite, several obstacles have to be overcome. The difficulty stems from the fact that the information in the topology and parameter files used in Charmm is contained in differently organized and formatted files in Amber, and not every feature in the Charmm force field has an obvious counterpart in Amber.

The solution for this problem calls for defining the system independently in Amber (e.g., using Leap) and establish the correspondence between the atom names in the original system and in the newly defined systems. After that, the file format conversion can be executed in such a way that the atoms are rearranged in the converted trajectory to the newly established order. Simulaid can establish the correspondence and make the conversion, including the rearrangement, but there are several steps on the way that the user has to perform 'manually'.