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 - 07:00:04 PDT
