[gmx-users] calculate interaction energy between two proteins

[SHAHEE ISLAM]

thank you so much.
now i understand this.

On 1/9/19, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 1/9/19 3:31 AM, SHAHEE ISLAM wrote:
>> it is connected with aggregation phenomenon.
>
> Maybe, but no force field is parametrized with protein aggregation in
> mind. Mark is cautioning you that you may be seeking a meaningless
> quantity.
>
> To calculate the interaction energy, you need to define energygrps in
> your .mdp file (each protein in a separate group), generate a new .tpr
> file, then use mdrun -rerun to re-evaluate the energies with these
> groups from the existing trajectory. Then it is your job to convince
> your skeptical audience that such a quantity actually means anything.
>
> -Justin
>
>> On 1/9/19, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>>> Hi,
>>>
>>> How is the protein-protein interaction energy defined? What physical
>>> observable is it connected to?
>>>
>>> Mark
>>>
>>> On Wed, Jan 9, 2019 at 9:03 AM SHAHEE ISLAM <islamshahee at gmail.com>
>>> wrote:
>>>
>>>> can anyone please tell me, if i select 42 then wheather it will
>>>> calculate the protein-protein interaction energy? because i did not
>>>> define two proteins in the mdp file.i just mentioned protein.I am not
>>>> understanding this.
>>>> thanking you
>>>>
>>>> On 1/8/19, SHAHEE ISLAM <islamshahee at gmail.com> wrote:
>>>>> hi,
>>>>> i want to calculate interaction energy between two protein.
>>>>> In my system there are two proteins,waters and ions.In my .mdp file
>>>>> the, energygrps               = PROTEIN W ION
>>>>> i am using this command
>>>>> gmx energy -f ../dynamic.edr -s ../eq.gro -o ener.xvg
>>>>> then the following options are coming
>>>>>
>>>>> 1  Bond             2  G96Angle         3  Proper-Dih.      4
>>>>> Improper-Dih.
>>>>>    5  LJ-(SR)          6  Coulomb-(SR)     7  Potential        8
>>>>> Kinetic-En.
>>>>>    9  Total-Energy    10  Temperature     11  Pressure        12
>>>>> Constr.-rmsd
>>>>>   13  Box-X           14  Box-Y           15  Box-Z           16
>>>>> Volume
>>>>>   17  Density         18  pV              19  Enthalpy        20
>>>>> Vir-XX
>>>>>   21  Vir-XY          22  Vir-XZ          23  Vir-YX          24
>>>>> Vir-YY
>>>>>   25  Vir-YZ          26  Vir-ZX          27  Vir-ZY          28
>>>>> Vir-ZZ
>>>>>   29  Pres-XX         30  Pres-XY         31  Pres-XZ         32
>>>>> Pres-YX
>>>>>   33  Pres-YY         34  Pres-YZ         35  Pres-ZX         36
>>>>> Pres-ZY
>>>>>   37  Pres-ZZ         38  #Surf*SurfTen   39  Box-Vel-XX      40
>>>> Box-Vel-YY
>>>>>   41  Box-Vel-ZZ                          42  Coul-SR:Protein-Protein
>>>>>   43  LJ-SR:Protein-Protein               44  Coul-SR:Protein-W
>>>>>   45  LJ-SR:Protein-W                     46  Coul-SR:Protein-ION
>>>>>   47  LJ-SR:Protein-ION                   48  Coul-SR:W-W
>>>>>   49  LJ-SR:W-W                           50  Coul-SR:W-ION
>>>>>   51  LJ-SR:W-ION                         52  Coul-SR:ION-ION
>>>>>   53  LJ-SR:ION-ION   54  T-Protein       55  T-W             56
>>>>> T-ION
>>>>>   57  Lamb-Protein    58  Lamb-W          59  Lamb-ION
>>>>>
>>>>> if i select 42 and 43. will it give me the total energy value
>>>>> considering both proteins.
>>>>> or what should i correctly select.
>>>>> thanking you
>>>>> Shahee Islam
>>>>>
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>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
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