Dear all I am trying to simulate a protein which a label (a small organic molecule) is covalently attached to a cysteine. Worth to say there is no label in the original pdb file of protein and it was attached to the Cys. using a software. Should I insert the label parameters into the conf.gro file or I need to modify a force field? If there is someone who has experiences in such systems, please have some advice.
Thanks in advance, Faezeh
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