Dear users,<br><br>I'm trying to compute the contribution of each residue to the total energy of a protein. I neutralized my system with 8 chloride ions and then made an index file with each residue in a different index group, using 'splitres' via make_ndx. it gave me an index file with atoms of each residue in different index groups. but as all these atoms are again listed in the default index group - Protein, grompp shouts out a fatal error. there was a post on the list about index groups being bungled up after taking the system thro genion. but i dont think genion really matters in my case. any inputs? my idea is to calculate the energy of each residue in a given protein. i wish to run a simulation for 10 ps for that. am i going wrong anywhere? is there a better way?
<br><br>thanks in advance<br>Kota.<br>