Thank you for the feedback. I am new to MD simulations so I tried to find a protocol that can lead me to understand how to build the topology,but I couldnt find. Do you know where I can find ?
Also, I found ffTK in VMD can generate CHARMM parameter file ,so I would like to know can I use cgenff_charmm2gmx_py3_nx2.py` script to convert my parameters obtained with FFTK into GROMACS format?
I found here ,someone has done it,Atom types equivalence between CHARMM36 and AMBER99bsc1
Thank you!
Udara