maybe they have a different orientation?I think there was a leap command
"alignaxes" that would rotate the system in the rectangular box.
I have not noticed this sort of issue using trancated octahedral box- is
there a reason you don't use solvateoct?
On Thu, May 26, 2011 at 9:44 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Thank you for this.
>
> The complex is NOT a larger structure. The two proteins have an identical
> residues of equal number. The ligand in both cases is the same.
>
>
>
> COMPLEX=loadpdb 2wc6_bal.pdb
> Loading PDB file: ./2wc6_bal.pdb
>
> total atoms in file: 1172
>
> Leap added 1079 missing atoms according to residue templates:
>
> 1079 H / lone pairs
>
>
> COMPLEX=loadpdb 2wch_bal.pdb
> Loading PDB file: ./2wch_bal.pdb
>
> Added missing heavy atom: .R<CTYR 141>.A<OXT 22>
>
> total atoms in file: 1171
>
> Leap added 1080 missing atoms according to residue templates:
>
> 1 Heavy
>
> 1079 H / lone pairs
>
>
> I'm a bit baffled by this.
>
> Thanks again
>
> George
>
> On May 26, 2011, at 3:36 PM, Carlos Simmerling wrote:
>
> > 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
> >>
> >>
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Received on Thu May 26 2011 - 10:00:03 PDT
