Hello, I am doing a refolding experiment, but I re-experience the same error. First of all, I use pdb2gmx for an input PDB structure, choose OPLS/AA force field and vacuum settings (no waters).
Then I amke a box, and start simulations. What I want to do is to compare the starting unfolded structure of the simulation and its changes during the sim (all represented as a traj.xtc) to a native folded conformation of the structure. Assuming it to be possible, I thought of using g_rms; g_rms -f native-folded.gro -s topol.tpr Then I get the same error message: WARNING: topology has 497 atoms, whereas trajectory has 491 ------------------------------------------------------- Program g_rms, VERSION 4.5.1 Source code file: mshift.c, line: 102 Fatal error: Molecule in topology has atom numbers below and above natoms (491). Thing is that both the topology and the trajectory are treated equally at the pdb2gmx step. So how can it be? Sergio
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