[AMBER] solvatebox

From: George Tzotzos <gtzotzos.me.com>
Date: Thu, 26 May 2011 15:20:25 +0200

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
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