What vdw and electrostatic parameters to use with Amber ff19sb

User discussions
1

GROMACS version: 2024
GROMACS modification: No

I am planning to run simulations using ff19sb by preparing the system entirely using AmberTools, then converting the final topology and coordinate files to GROMACS format using ParmEd. However, in looking at the description of FFs in GROMACS, the CHARMM section says the following:

For using CHARMM36 in GROMACS, please use the following settings in the mdp file:
constraints = h-bonds
cutoff-scheme = Verlet
vdwtype = cutoff
vdw-modifier = force-switch
rlist = 1.2
rvdw = 1.2
rvdw-switch = 1.0
coulombtype = PME
rcoulomb = 1.2
DispCorr = no

There is no comparable section for AMBER FFs, but the wording seems to imply that these values are to be used only with CHARMM36. What are the default values for these, and/or what values should be used with ff19sb?

2

Hey,

you should not used the non-bonded interaction parameters specified for the CHARMM36 FF with the AMBER FF. There was a discussion about which parametes are needed for the AMBER FF here.

Also you can not use ParmEd to convert a ff19sb topology to GROMACS format (see here and here.

A possible alternative to generate a ff19sb topology in the GROMACS format would be CHARMM-GUI or using a script to convert the AMBER ff19sb topology to a GROMACS topology.

3

Hi Eddie,

Thanks so much for your advice and all the references! I will try using the script in your last link to convert the topology.