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Hello
Im havng lots of problems with generating topology for non standard molecules ( silica nanoparticles ) in gromacs
I have modified oplsaa force file atomtypes.atp and atomname2type.n2t and used x2top command and every time i run into this errors : Could only find a forcefield type for 0 out of 11616 atoms
& Can not find forcefield for atom SI1-17150 with 3 bonds
can anyone tell me how to do it?
ps: I would appreciate if anyone could suggest a free program for building nanoparticles
Instead of relying on the x2top command to automatically generate your topology files, you might consider manually editing your topology file by creating separate .itp files for the force field parameters and including them in the topology.
For building the nanoparticle, VESTA software is a good choice for visualization and manipulation of crystal structures. However, I used the ASE package in Python (from ase.build import bulk) to create your structure, and then cut the specific radius for the particle.