Generation of topology for non-standard molecules



Periodic distances are considered by default, so if these are the atoms causing problems, it means your box size is incorrect (perhaps too large such that the distances are not recognized as satisfying the criteria specified in the .n2t file).

Thank you for the help… But I will one last question here. I am getting problem due to a certain portion of bond. For example, I have defined an atom name OB and its atom type is OA. When I am running the x2top command, half of these are creating problem. I have looked at their bond lengths using both avogadro and materials studio and filled them accordingly, but still facing some error. Why is that only half of them is creating problem. Like I have 8 OB atoms, of which 4 are creating a problem with no forcefield found.

There’s not much more I can add beyond the suggestion I have already made. You will need to look at those atoms and determine what their nearest neighbors are, including across boundaries.

Im having same problem with silica nanoparticles and dont know how to parametrize them and generate toplogy if you have overcome the issue could you please email me the the solution?