[gmx-users] convert amber topology and coordinates files into gromacs topology

[Ming Tang]

Dear list,

I am studying glycoprotein. As amber is very slow on CPUs, I really want to do my simulations in gromacs. I found that gromacs has amber99sb.ff. So I want to convert amber topology and coordinates files into gromacs topology using Antechamber. My concerns are:

1)      amber16 has leaprc.protein.ff14SB now, then is it reliable to study my glycoprotein using amber99sb.ff in gromacs?

2)      If amber99sb.ff in gromacs is reliable, will the topology changing process using Antechamber affect the simulation results?

Thank you,
Tammy