Hi everyone. I'm doing some simulations of a phosphorylated peptide. Right now, I'm using the amber force field with some parameters that were obtained for charged phosphorylated amino acids in a paper I found. Now I want to simulate uncharged phosphate groups, but the paper only gave parameters for -1 and -2 charge states. I'm stuck on this. I'm only missing two bond parameters. They are the OH-P-OH angle and the HO-OH-P-OH dihedral, where the atom type names are shown below: O2 (-) | |R-P-OH-HO | | O2 (-1 charge) O2 | |R-P-OH-HO | OH | HO(neutral) Is there some way of getting these parameters? Once that is done, I still would need to assign charges. Does anyone have any idea what the best way forward would be? I would prefer to stay in the amber force field, but if that's not possible I'm open to others. Thanks for your time!
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