[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [modeller_usage] NaN error model generation Lennard-Jones restraints



On 3/11/11 3:07 AM, David Rodríguez wrote:
Taking Nick's advice into account, I switched on the dynamic
Lennard-Jones restraints with the simple script shown below. Some models
are generated, showing improved statistics regarding clashes and
stereochemical quality, but many others fail to be generated due to NaN
values in the optimization process
That doesn't sound surprising - LJ will blow up if any pair of atoms get 
too close together, and many of the randomized initial models are likely 
to have such clashes. You could building models in the regular fashion 
and only then refining them with LJ, or modifying the randomization 
method to avoid introducing clashes. But what you're doing already 
sounds fine - just build models and discard the ones that fail with NaN.
	Ben Webb, Modeller Caretaker
--
modeller-care@salilab.org             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage