i am using modeller 8v2 version on pentium IV workstation
so how much time it may take to optimize the protein containing
two chains, having length of 423 amino acid residues on the workstation
i am using currently
It will probably take about 10-30 minutes. The easiest way to find out
is to run it...
what is time requirement if i use SGI, IRIX
6.5 fuel work station for the same using default parameters in modeller?
An SGI IRIX box is probably about 10 times slower than a modern PC.
another thing i want to know is, which is the preferred method to obtain
the best result after MD, whether i should go for the final model after
all the steps of MD or the least energy model out of all the possible
conformations it generated?
The default Modeller procedure is to take the final model, and we find
that works well.