Thanks Carlos and all the other contributors,
You've answered my query. Concerning solvateoct, I didn't use it because of a bad habit.
Best regards
George
On May 26, 2011, at 6:41 PM, Carlos Simmerling wrote:
> 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 - 13:00:02 PDT
