Hi, gmx-users, I have a problem to "translate" nitrogen base residue names from AMBER to GROMACS. I have simulated with AMBER a DNA-protein complex, then i have changed in the prmtop file the standard nitrogen bases as DT--> DTHY, DG-->DGUA, DC-->DCYT, DA-->DADE, in order to "translate" the MDs from AMBER to GROMACS... but in the prmtop file are present also DT5, CT3, that indicate the residues at the end of the chains... anyone knows which is the correct GROMACS residue name for these residues? I have searched in the ff.rtp file but seem that these particular residues are not present... Thank you in advance...
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