the vof the first box is much bigger so it needs more water. you don't
really say whether the complex is a larger structure (dimensions) or not.
Leap seems to think it is.
On Thu, May 26, 2011 at 9:20 AM, George Tzotzos <gtzotzos.me.com> wrote:
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 26 2011 - 07:00:03 PDT
