Questions and problems?

Neutral ASP, GLU

Please let me know if edit can generate hydrogen of COOH in GLU. When I used AMBER4.0, generated files did not contain H in the carboxyl group. It is important because GLU and a sugar oligomer binds by hydrogen bonding in my calculation. Thank you in advance.

You want to use the "GLH" residue (glutamic acid neutral form), rather than GLU in link. Then edit will construct the proton for you (in a somewhat arbitrary location, but generally fine for subsequent minimization or dynamics work.)

Same idea for ASH, the neutral form of ASP.