Hello gmx-users I am trying to simulate an amino acid (say GLN). It can be as a zwitterionic form or uncharged ends. Neither ffamber or ffopls force fields has a complete parameter for them. While in ffamber, I have the parameters for CGLU and NGLU, but not for a Glutamine. Do I need to define it there, or there is some way out. If I need to define it, how do I retrive the partial charges.
Any insight would be very helpful. Thanks Chandan -- Chandan kumar Choudhury NCL, Pune INDIA
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