[gmx-users] Problem with DNA chain

[Marco Deriu]

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