Dear Amber's users!
I want to perform list of full atomic simulation of protein-ligand
complexes in Gromacs using Amber99sb force field and ligand parametrized by
means of antechamber (acpype).
1- From antechamber tutorials I've found that GAFF is used for such ligand
parametrization. What cut-offs for electrostatics as well as vdw should I
use for the modelling of protein-ligand complexes ? (assuming that I've
used 1.0 cutoffs with such systems without ligands)
2- How I can assign charges more carefully ? Could you provide me with some
example of such charges assignment based on different chemical compounds?
Thanks for help,
James
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Received on Mon Apr 08 2013 - 05:00:03 PDT
