I would like to do classical MDS of a protein containing phosphorylated cysteine (3-oxoalanine) using GROMACS. Which force field should I use?
pCys and 3-oxoalanine are two distinct noncanonical amino acids. Neither is supported in any force field I know of. You'll have to derive parameters yourself.
Thank you respected professor Justin Lemkul !!! When you mean "derive parameters yourself", Are you suggesting me to use external parameter retrieval such as ATB server?
If you do, be very careful. Servers do not generally produce as high-quality of topologies as you will need for an intrinsic residue. Pick a force field with a well established parametrization methodology (GROMOS is lacking in published detail, in my opinion, but choose whatever you think will work best) and derive the parameters in a manner consistent with the parent force field. This is not a trivial task. Expect to expend significant effort; if the model is inadequate, any subsequent simulation is a waste of time.
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