James Starlight wrote:
Dear Justin,
After 20 iterations I've obtained structure like this
http://www.sendspace.com/file/gyyj38
I suppose that this variat is more closely to correct form :)
I can't access the file, so I don't know. 20 iterations still doesn't sound
like enough for the tutorial system, unless you shrunk faster than what was
recommended.
But during solvation via GenBox I've obtained that error
One of the box vectors has become shorter than twice the cut-off length
or box_yy-|box_zy| or box_zz has become smaller than the cut-off.
Where I can change that cut-off distance?
There is no reason that your system should be this small to trigger this error.
The box dimensions should be on the order of 6 nm. genbox uses a search
radius for deleting overlapping molecules. Perhaps the value you have set in
vdwradii.dat for C radii is too large for genbox to function properly. Without
more detail, I can't suggest anything else. The procedure in the tutorial
should work; I've run through it dozens of times. Please pay careful attention
to all of the values specified in all of the necessary files and commands.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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