[gmx-users] Problem with AMBER-GROMACS DNA database residue

[Rubben Torella]

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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