I will try as per your directive.
But, this problem is similar to one problem, which I found by searching 'NaN' in mailing list archives.
Actually , I am using one alignment and it finely generates 50 strs but in this particular case when I removed some terminal residues of target sequence, which I dont want to model, it gives this error. So there is a very minute change in alignment, and it produces this error and these removed residues are terminal residues of target sequence.
Please have a look to weblink and suggest some more options if possible although I will try your advice.
Quoting Modeller Caretaker firstname.lastname@example.org:
> vivek sharma wrote: > > 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. > > Ben Webb, Modeller Caretaker > -- > email@example.com http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >