Hi everybody,
I'm dealing with two protein models (2wc6 and 2wch) representing the same protein. The first crystallographic model is the protein + ligand whereas the second is the apo-protein.
I've run MD on both with the same ligand and under the same conditions.
For 2wch
solvatebox COMPLEX TIP3PBOX 12.0
Solute vdw bounding box: 42.862 46.736 48.736
Total bounding box for atom centers: 66.862 70.736 72.736
Solvent unit box: 18.774 18.774 18.774
Total vdw box size: 69.814 73.396 75.927 angstroms.
Volume: 389057.601 A^3
Total mass 190444.906 amu, Density 0.813 g/cc
Added 9645 residues.
whereas for 2wc6
solvatebox COMPLEX TIP3PBOX 12.0
Solute vdw bounding box: 42.462 39.736 42.736
Total bounding box for atom centers: 66.462 63.736 66.736
Solvent unit box: 18.774 18.774 18.774
Total vdw box size: 69.529 66.696 69.404 angstroms.
Volume: 321847.802 A^3
Total mass 154629.098 amu, Density 0.798 g/cc
Added 7657 residues.
My question is why is there a discrepancy of some 2,000 water molecules?
Thanks for any suggestions
Regards
George
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Received on Thu May 26 2011 - 06:30:02 PDT
