Follow the links (attached herewith).

http://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-tutorial.pdf

https://www.sciencedirect.com/science/article/pii/S0006349503750905

Thanks,

Amin

If your modification corresponds one of the post-transnational amino acids then you can use the PTM server. The force field parameters are also given in this web server. follow the link: http://vienna-ptm.univie.ac.at/

paramchem.org is good for an initial parameter file in CHARMM.

There is a good server for it..LigParGen..it generates parameters using CM1 methods (quantum mechanics) and build the topology for a lot of force fields , also it has tutorials . I use it for OPLS .

If you want parameters for modified peptides you should use the tutorial of CHARMM for it..it's very good