Dear all!

Sometimes I need to build a models (homology or via threading). After these procedures (on different servers) usually I check results by myself. Usually I do Protein health with "check structure" and "calculate energy" protocol (CHARMM). I became observe a strange thing. For instance I get a geometry report with 3 noncritical errors and energy report with 2000-3000 kcal\m. Further minimization gives the energy less then -1000 kcal but geometry became worse - with 12 noncritical and 2-3 critical errors.

   At the same time Swiss PDB shows very good negative energy (GROMACS) before minimization.

Can anybody explain this phenomena?