Thanks Maik for your parameters for amber99 soft core !
Berk, you were right. The missing term is indeed the one associated to the use of constraints=all-bonds. And yes, there was a mistake in my .top file... May I ask an other question ? I still have a warning message with grompp : "WARNING 1 [file "XXX.itp", line 3451]: Some parameters for bonded interaction involving perturbed atoms are specified explicitly in state A, but not B - copying A to B" where as the line 3451 is (dihedral) : 175 177 178 187 1 nucleic_imp_10 nucleic_imp_10 nucelic_imp_10 being defined in ffamber99bon.itp. It seems to me that the state B is explicitly specified. How to get rid of this warning ? It does what I want anyway, but I want to understand what is happening. Thanks, Michaël Bon
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