Hi George,
Notice that, in LEaP, you have *NO* control over the number of water
molecules that will be added to your system. The number is calculated
to fill the box where the smallest distance between any wall and any
atom of your molecule is at least the buffer you provide, in your case
12 Angstroms. If the 2 structures are not exactly the same (in space),
then they will end up with different numbers of water molecules.
In your case you have the protein in two forms so, even if the
sequence and number of atoms is the same, they occupy different
volumes, and will lead to different size boxes.
If you need them to have the same number of waters, you can tinker
with the buffer size of the smaller system until you get the right
number.
HTH,
Gustavo Seabra
Professor Adjunto
Departamento de Química Fundamental
Universidade Federal de Pernambuco
Fone: +55-81-2126-7417
On Thu, May 26, 2011 at 10:20 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
>
>
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Received on Thu May 26 2011 - 09:00:05 PDT
