[gmx-users] Atom O5' not found in residue seq.nr. 1 while adding atom

Dear Gromacs Users, I m trying to simulate a DNA structure with amber03 force field. However, when I give first command of pdb2gmx. Following error comes: Fatal error: Atom O5' not found in residue seq.nr. 1 while adding atom. As O5' is present in DA nucleic acid. So,I

[gmx-users] Atom O5 not found in residue seq.nr. 1 while adding atom

Dear Gromacs Users, I need to simulate a protein that has N-acetyl glucosamine (NAG). Since NAG residue is not present in residue topology file, first of all i added NAG parameters to aminoacids.rtp file. I am following this link *