Hi,
I'm a Gromacs user I am working in this moment on DNA chain. I created a pdb
file using Hyperchem, I performed a pdb2gmx and I obtained the top and gro
files. I noted the fact that from the top file are missing all the
connection terms (bonds, angles, dihedrals) between nucleotide monomers. For
instance, in the ATC sequence the bond term between A-T and between T-C are
missing. I would need some help in order to understand if it is necessary to
modify the Termini Database (ffG43a1-c.tdb,ffG43a1-n.tdb) or something else.
Thank you.
Best regards,
Marco Deriu
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