On 07/17/2009 10:03 AM, Cool Hunk wrote: > as i was trying to refine the loops using dope_loopmodel() method, it > has generated following error > " check_inf__E> Atom 1 has out-of-range coordinates (usually infinity). > The objective function can thus not be calculated." > but when i used only loopmodel() method it has generated loop models, is > thr any way of handling this error or what does it mean.
dope_loopmodel, unlike the regular loopmodel, includes implicit solvation (GB/SA). This method can sometimes run into numerical instability with certain conformations, leading to huge forces on your system. Usually the simplest solution is to simply build many loop models and discard those that have this problem.
Ben Webb, Modeller Caretaker