Dear Gromacs Users, My Protein has three N-acetyl glucosamine (NAG) residues, UDP and Mn. I have to simulate this protein. I am using a gromacs version of 4.5.3. When i did pdb2gmx step, i understood that NAG is not present in the residue topology database. I used GROMOS96 53a6 force field as i am going to use topology of UDP from prodrg server. I understood that i have to add parameters regarding NAG in aminoacids.rtp, aminoacids.hdb, ffbonded.itp, gbsa.itp and residuetypes.dat. But i am not able to understand what should i mention. Could any body of you please help me out in solving this problem. Thanks in advance.
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