Hi there! I’m running simulation of a protein containing extended intrinsically disordered regions.
I want to use the amber99sb-disp force fiels, that is the state of the art force field for intrinsically disordered proteins, but that also considers ordered regions ( Robustelli P, Piana S, Shaw DE. Developing a molecular dynamics force field for both folded and disordered protein states. Proc Natl Acad Sci U S A . 2018;115(21):E4758-E4766. doi:10.1073/pnas.1800690115 )
It was developed using Desmond, but they converted it to be GROMACS compatible.
It simply uses a tip4p model with increased dispersion corrections.
The problem is that I get these WARNING when I run the equilibration phase with only a box of water (to benchmark it):
WARNING: There are no atom pairs for dispersion correction
Long Range LJ corr.: 0.0000e+00
Someone knows how to deal with this problem?