[gmx-users] calculate interaction energy between two proteins

[Justin Lemkul]

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
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