[gmx-users] Using x2top and grompp

[Devon]

> My goal is to get a topology.tpr and trajectory.xtc in those file formats. I’m starting off with .pdb, .xyz, and .gro files of an experimentally determined crystal structure. The crystal contains two kinds of molecules that interact via halogen bonding. i do not want to run these molecules in a solvent. i produced a topology.top file using x2top but when i tried to use grompp to produce a tpr and i only got an mdout.mdp. what am i doing wrong? I’m willing to start over completely. I also need to know how to run my crystal without a solvent.
> 
> Thank you