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<br>Thanks for the reply ! <br><br>I have tried building the topology with generating the index file <br><br>make_ndx -f * <br><br>it gave options i have selected the protein and the solvent <br><br>then i gave minimization <br><br>in the minimization file i have included <br><br>energygrps = Protein SOL , <br><br><br>but the energy file have the same when i removed and inserted the above flag ! <br><br>if any one can explain me in detail it will be helpfull <br><br>thanks in advance ! <br> </div></body>
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