Hi, Respected AMBER users, hope you are doing well. I need advice about using name for cysteine residues. In manual, there is no mention of CYM for depronated cysteine residue, while in tutorial, it's written. If I use CYM as name for depronated cysteines as determined by H++ server, then in creation of prmtop and inpcrd files, leap shows correct charge as determined by H++ server, while if I change CYM to CYX to avoid leap hydrogenating them, then leap tells that there is unperturbed charge. In both cases I added Na+ to neutralize it as protein has -6 charge on pH 7.4 determined by H++ server. Wanna ask should I use CYM or change it to CYX?
Please see leap files attached.
Thanking you in advance for your help.
Kaleem Arshad
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Received on Tue Feb 13 2024 - 20:00:02 PST
