Hi everyone,
I am currently trying to perform MD simulations of p-glycoprotein with N-glycans attached to it, but I am having some issues while creating inpcrd and prmtop files via xleap. I have attached glycans via GLYCAM_web but when I load the pdb file into xleap, it shows several missing bonds among the glycan chains including the covalent bond between ASN and GlcNAc. Moreover, when I draw the missing bonds in xleap it gives missing bond, angle and torsion parameter errors. I have been trying to fix this issue but couldn't get any luck. Any help to solve this issue is highly appreciated.

Kind regards,
Mahrukh Imtiaz
COMSATS Institute of Information Technology
Islamabad