I am a regular user of MODELER and I use 6v2.
But now when I was generating 50 structures of a target using some
templates, program ran fine till generating first 28 structures but died
in 29 structure generation with the error mentioned below (please see
below).
For, the first time I have observed this error. What can be the problem.
In the last statements of optimization schedule in log file you can see
the current value of energy is mentioned by 'NaN'. What does this mean,
looks like 'energy' has gone out of certain limits.
NaN is 'not a number', and you're right - it probably means that the
energy has increased so much that it's gone out of the limits of the
datatype. You probably have a very bad initial structure, or an odd set
of restraints - you could try a short initial optimization to relax the
structure before trying to build your model.