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Greetings,
I would like to use CHARMM-GUI to generate input files for a GROMACS molecular dynamics simulation. However, my protein contains selenocysteine (SEC), which is not supported by CHARMM-GUI. The tool recommends replacing SEC with cysteine, but the selenium ion is critical for the function of my protein, so I cannot make that substitution.
I need to generate the necessary parameter and topology files, but I have no prior experience with this process. I came across this link (AMBER-parameters-database/sec_derivatives/SEO.off at main · MALBECC/AMBER-parameters-database · GitHub)], but I’m having trouble understanding or using the information provided there.
Could someone please guide me on how to proceed with generating appropriate parameter and topology files for a protein containing selenocysteine, ideally for use with GROMACS?