AMBER99sb-ILDN with Slipids

User discussions
1

GROMACS version: 2020.3
GROMACS modification: No
Here post your question I am using amber99sb-ildn to model a membrane protein and Slipids (2020 w/ torsional parameter updates) for the membrane description. In the original D.E.Shaw paper of ILDN it seems they use a cutoff of 1.0 nm for non bonded interactions whereas the Slipids most recent publication uses a 1.4 nm cutoff for electrostatics (https://pubs.acs.org/doi/10.1021/acs.jpcb.0c06386). It is thought that Slipids has the same parameterisation philosophy as the amber family of force-fields and therefore can be used together. However it is not clear to me what cutoffs and parameters I should primarily follow to study protein-ligand interactions mainly.

Thanks for your help.

Dimitris

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I’ve tested a 1.0 nm cut-off for Slipids with POPC and it behaves fine (see Figure S2 of ). While Slipids does say that it is compatible with AMBER protein force fields, not all of the parameterisation processes completely match. There are other options you could choose but I guess it depends on what you trying to do. Cheers Tom