I have just started working in the field of molecular dynamics and using gromacs for my studies. The problem that I am facing is topology generation for non-standard molecules. I looked into the gromacs manual on how to add residue to a forcefield but that is quite confusing. I started with a simple methane molecule and tried the command x2top as well by putting in some values for the force constants, but I got an error over there as well. How can I go about generating the topology. It would be helpful if someone could show with an example.
And I don’t want to use the external servers like ATB or cgennff etc as the values they take for the parameters are always accurate. Moreover, they also have a limitation on the number of atoms that can be present in a structure. I am working inorganic slabs like silica etc. so my sample will have large number of atoms. I have created the slab using materials studio and converted it into a pdb file. Now I don’t know how to proceed.
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