[gmx-users] dna-ligand simulation

[sarah k]

Dear all,

1-   I’m trying to simulate a DNA-ligand complex. I have to use AMBER force
field for the DNA structure. I have used PRODRG to get the required files
and parameters of my ligand. PRODRG generates GROMOS based files.
Consequently, when I add the ligand to my ligand topology and coordinates
to DNA files, Gromacs can’t recognize some atom types in AMBER force field.
Can I expect such simulation to give reliable results? How can I solve the
problem?

2-   I would like to save my final *.gro file during md simulation step
after each 0.5 ns. How can I do so?

Thanks and regards,

Sarah Keshavarz