Thank you Jason
Given that vdi + Electrostatic = 0 (WHY?) would it be correct to say that this terms equals the salvation energy (polar + non polar) of the residue?
George
> On 05 May 2016, at 03:03, Jason Swails <jason.swails.gmail.com> wrote:
>
> On Wed, May 4, 2016 at 3:27 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> Apologies if this has been answered earlier in the list. I searched to no
>> avail.
>>
>> The output of pairwise per-residue decomposition shows the interaction
>> energy of a particular residue with itself, e.g.
>>
>> Resid 1
>> Resid 2
>> Internal
>> van der Waals
>> Electrostatic
>> Polar Solvation
>> Non-Polar Solv.
>> TOTAL
>> ARG 220
>> ASP 78
>> 0.00
>> 0.11
>> -34.32
>> 29.88
>> -0.46
>> -4.79
>> ARG 220
>> GLU 74
>> 0.00
>> -1.05
>> -23.03
>> 21.20
>> -0.61
>> -3.49
>> ARG 220
>> ARG 220
>> 0.00
>> 0.00
>> 0.00
>> 2.79
>> 0.52
>> 3.31
>>
>> I’d appreciate if someone shed some insight as to the significance of this.
>>
>
> It's the sum of all interactions between two atoms within that residue.
> Keep in mind that this is GB, so there is no self-energy term like you get
> in Ewald-based methods.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
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Received on Thu May 05 2016 - 03:30:03 PDT
