I have a engineered residue (a chromophore) in my protein. I have the gromacs formated topology file for this and was trying to modify the library.py script of PMX but it seems very tedious and prone to mistake. Is there any straightforward way to do this?
I would suggest to create an .rtp entry for the chromophore, add it into aminoacids.rtp and continue following the standard scheme for hybrid structure/residue generation, e.g. see Figure 3 in this book chapter http://www3.mpibpc.mpg.de/groups/de_groot/pdf/Aldeghi_CMPE_2019.pdf
Thanks so much its working now.