Hello,
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
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Thanks so much its working now.
Continuing with @nandanhaloi123 question, is it the same way I should proceed with the residues that are erstwhile defined in the regular force field by adding those .rtp entries it to the mutated force field .rtp file?
Moreover do I need to add that residue in the library.py file.
You need to add an .rtp entry of a hybrid topology to the mutres.rtp and mutres.mtp files. I don’t think that changes in the library.py are needed for that.