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Hi All, One of my ARIA/CNS runs has just finished and the result is rather bizarre. All atoms of my structure are dispersed as if all bonds were not recognized during the water refinement. All 100 structures from the 8th iterations are OK (same goes for every other iteration). Now, I have a modified residue incorporated into my sequence, so my parameter, topology, linkage and generate.inp files are slightly diffrent, but only by means of adding new lines not modifying in any way existing ones (Acetyl and NH2 caps are introduced as well). I can send you my modifications (they were introduced in collaboration, so not all of them are strictly speaking mine), but maybe you have a hunch what is going one already. What is surprising is that although the modified residue is a part of my peptide, the protein atoms (I am trying to calculate a structure of a complex) is also equally destroyed, creating quite pretty galaxy in pymol. I have to mention that before the parameters, topology etc. modifications were introduced I run a simulation on the same complex, but with unmodified residue and had no problems with refinment, so those must be the modifications that made it inpossible to water refine my structure. All ARIA settings are standard apart from cooling and refinement steps of MD + I am using a preliminary structure as a template for MD. Again thanks in advance for any suggestions, Piotrek