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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 ImtiazCOMSATS Institute of Information TechnologyIslamabad