Dear All,
While creating a solvent box I followed the following steps :
x= loadpdb tem.pdb
alignaxes x
set x box 10
set x restype solvent
desc x
UNIT name: Molecule
Head atom: null
Tail atom: null
Periodic box: 10.00000, 10.00000, 10.00000
Contents:
R<SUBUNIT 1>
solute =loadpdb ccl.pdb
solvatebox solute x 10
Solute vdw bounding box: 42.058 199.760 29.041
Total bounding box for atom centers: 62.058 219.760 49.041
Solvent unit box: 10.000 10.000 10.000
Total vdw box size: 47.193 218.991 43.896 angstroms.
Volume: 453655.599 A^3
Total mass 63122.844 amu, Density 0.231 g/cc
Added 410 residues.
Here my question is that though it solvates my solute , the solvent box is
not equilibrated .
If I go for solvatebox solvent solvent 10
The solvent molecule is at center surrounded my other solvent molecules.Will
it be the proper initial structure for the equilibration steps .
Please suggest .
Thanks
John.
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Received on Wed May 19 2010 - 11:30:03 PDT
