GROMACS version: 5x
GROMACS modification: Yes/No
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I have been trying to simulate a DNA in a membrane using KALP-15 tutorial.
The Gromos 53a6 force field is not being able find Adenine ‘residue topology database’.
The Adenine is denoted as DA in the pdb. How can I check what naming procedure to use to make the DNA bases match with Gromos topology database ?
The GROMOS force fields (as implemented in GROMACS, at least) do not support nucleic acids.
The most reliable force fields for nucleic acids are AMBER and CHARMM. I hardly ever see anyone use GROMOS for simulations of nucleic acids.
Thank you for the response.
Is there any guidelines available regarding how to use berger lipid with amber99 force field ?
The Berger lipids are quite outdated. AMBER Slipids work very well if you’re using the AMBER force field. Note that ff99 is also outdated with respect to AMBER nucleic acid parameters. GROMACS doesn’t have the latest (best) parameters (parmbsc1) but maybe someone has produced a port for it.