ligand parameterization in gromacs
Does SAMSON parameterize ligands itself like YASARA structure? or is there any way to parameterize ligands in automated mode (as i do not know ligand parameterization).
Not at the moment, but some users have obtained parameterizations from https://atb.uq.edu.au/.
Thanks for the link but I tried this too. I does not work all the time. But as I mentioned in YASARA structure, parameterization is a childs' play. How they do it is secret for me but it is kool.
If there will be something like that in SAMSON too, it will be very easy to run complex simulation affectively.