Hi,

I just finishing running some simulations in NAMD on a protein-ligand system, which gave me a DCD file as output. I am now using GROMACS to produce multiple pdb files from this dcd. I would like to calculate the binding energy between a molecule and the protein for all of these pdb files. The problem is that I have to set the molecule as its own parent in order to run (right now the molecule is under the same parent as the protein), and then I can choose the "system:Selected" for my input ligand. Is there a script or protocol that can automate this process, so I don't have to manually go through 100+ pdb files, set the parent, and calculate the binding energies? If not, how would I begin writing such a script? Thanks for all your help.

Deren