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Dear Members:
 because my residue in the protein is a non-normal amino acid ,so the AMBER can
 not recognize it .I want to fit the charge . but I can not determine what
 structure I use? Is I use the whole residue which have the normal COOH and NH2
 or I use the structure which deleted OH and H(NH2) ? Can anyone give me
 suggestion about how to calculate charge of it ?
 Best regards!
 Xiong Bin
 Shanghai Institute of Materia Medica, C.A.S.