On 14/02/2012 4:57 PM, James Starlight wrote:
Justin,
Firstly I've created the box of desired size with only 500 molecules (
I need 1000)
Than I've tried to add extra 200 molecules by means of Genbox
genbox -cp super_box.gro -ci Ccl4.gro -nmol 200 -o new_solv.gro
but no molecules have been added
Added 0 molecules (out of 200 requested) of Cl4
... then there are no gaps large enough to insert your molecules. Either
make gaps, or check out genbox -h for advice on defining the radii.
also I've tried
genbox -cp super_box.gro -cp Ccl4.gro -nmol 200 -o new_solv.gro
Two -cp options is not what you want, and -nmol probably only works with
-ci.
but system were crashed with message
Reading solute configuration
God Rules Over Mankind, Animals, Cosmos and Such
Containing 2500 atoms in 500 residues
Initialising van der waals distances...
WARNING: masses and atomic (Van der Waals) radii will be determined
based on residue and atom names. These numbers can deviate
from the correct mass and radius of the atom type.
Reading solvent configuration
"God Rules Over Mankind, Animals, Cosmos and Such"
solvent configuration contains 5 atoms in 1 residues
Is there any ways to add extra mollecules to the pre defined box ?
Yes - but there has to be room for them.
Mark
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