[gmx-users] Software for PDB input for GROMACS

[Dan Gil]

Hi,

I would like to use the parmbsc1 force field to simulate DNA. I installed
the force-field and am now actually running a simulation with a Drew
Dickerson Dodecamer structure I downloaded from the RCSB database.

Now I would like to generate my own structures and simulate them. I tried
using Avogadro, but the software is not following the same conventions as
parmbsc1 and therefore failing at pdb2gmx.

Do you have recommendations on how to generate a PDB structure for nucleic
acids? I suppose I could do this by hand, but I would very much like to
avoid this path if I can.

Best Regards,

Dan