Dear Sir,
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.
http://salilab.org/archives/modeller_usage/2002/msg00189.html
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.
regards,
Vivek
Quoting Modeller Caretaker <>:
> 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
> --
> http://www.salilab.org/modeller/
> Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
>
--
VIVEK SHARMA
"You must be the change you wish to see in the world."
MKG