I generated parameters for the molecule attached to be used in Q6. I was surprised about the small Avdw value obtained for carbonyl . carbon 1059.1297 rather than 1802. I wonder the reason for such assignment.
In the itp gromacs file the same happens, the value does not correspond to the one observed for example in ASP.
Moreover, several torsions seems to be missing, which in reality exist for such group. Using ffld those parameters seems correct, but not with ffld
I believe this to be a bug with LigParGen
Issue Information
I generated parameters for the molecule attached to be used in Q6. I was surprised about the small Avdw value obtained for carbonyl . carbon 1059.1297 rather than 1802. I wonder the reason for such assignment. In the itp gromacs file the same happens, the value does not correspond to the one observed for example in ASP. Moreover, several torsions seems to be missing, which in reality exist for such group. Using ffld those parameters seems correct, but not with ffld
test-lig.zip
Many thanks in advance for your help
Fernanda Duarte Associate Professor of Chemistry Chemistry Research Laboratory Mansfield Road University of Oxford Oxford OX1 3TA UK