Hello all I obtained a top file after running the "amb2gmx.pl" script,but I feel some errors in this top file. The functype of the [dihedral] is 3 in this top file,but the [pairs] part aslo presence in it. And the manual is point that "with the Ryckaert-Bellemans potential the 1-4 interactions must be excluded from the non-bonded list." So I think this top file is incorrect? Could you give me some opinion? Force field is amber03 in gmx4.5.1,ligand is disaccharide. Thanks !
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