[gmx-users] Residue 'NAG' not found in residue topology database

pragna lakshmi pragnapcu at gmail.com
Thu Mar 8 09:14:35 CET 2012

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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