Recently I have been working on Linear combination of Distance (LCOD). One has to extract a set of structures (may vary from 100 to 1000 to any bigger number depending on requirement, accuracy) from a very long trajectory. If one is looking for very specific orientation, then it is necessary to go through the whole trajectory and choose the required frames and select that geometry, which is very tedious and time taking job. But more often a random selection from the trajectory is done to take care of all the diversity in the trajectory. In Amber, one can use ptraj to select a frame from trajectory and created its restart file to launch LCOD calculation. To launch such 100 or 1000 calculation one need to modify or create 100 or 1000 such input files to feed to ptraj with the frame number and the name of the restart file. I am using a dictionary in python to do so. Beginning with 2 lists: one having frame numbers to be selected another with name of the restart files correspondin
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