Dear Eduardo,
the current AmberManual (version 20, section 32.11.41) answers your
question:
"For each frame, calculate the non-bonded interactions between all atoms
in <Ligand mask> with all atoms in <Surroundings mask>. Electrostatic
and van der Waals interactions will be calculated for all atom pairs."
Thus, the pairwise energy contributions between the two sets of atoms
are calculated. This is a very fast energetic analysis for post-processing.
(For calculation of an interaction energy via an energy difference,
MM/GBSA can be used, which is, hower, more expensive.)
Best regards,
Anselm
On 03/09/2021 11:33 PM, Eduardo R. Almeida wrote:
> Dear Dr. Anselm Horn,
>
> Regarding the function LIE (linear interaction energy) from cpptraj for calculating the interaction energies between two masks, the results generated from this analysis refer to either an energy difference (DEAB = EAB - EA - EB ) or the absolute energies (EAB) ?
>
> Sincerely,
>
> Eduardo.
>
>
>
>
>
>
> ________________________________
> De: Eduardo R. Almeida <eduardoe.r.a.hotmail.com>
> Enviado: terça-feira, 9 de março de 2021 17:04
> Para: AMBER Mailing List <amber.ambermd.org>
> Assunto: Re: [AMBER] Pair interaction energy
>
> Dear Dr. Anselm Horn,
>
> Thank you for you response! I will test this function (lie) with my system.
>
> Best regards,
>
> Eduardo.
>
>
>
>
>
>
> ________________________________
> De: Dr. Anselm Horn <anselm.horn.fau.de>
> Enviado: terça-feira, 9 de março de 2021 16:50
> Para: amber.ambermd.org <amber.ambermd.org>
> Assunto: Re: [AMBER] Pair interaction energy
>
> Dear Eduardo,
>
> maybe the linear interaction energy feature from cpptraj is what you are
> looking for. The name of the command is lie, and you can specify two
> masks, between which the interaction energy (vdw, ele) is computed for
> each frame of the trajectory specified.
>
> Regards,
>
> Anselm
>
>
> On 03/09/2021 03:53 PM, Eduardo R. Almeida wrote:
>> Dear Amber users,
>>
>> I would like to know if there is a function in cpptraj to calculate the pair interaction (van der Waals + electrostatic) between two entities over a trajectory. In the manual (Amber 18), I saw the pairwise function, but I do not know if this function calculate the pair interaction energy, since I did not see how to specify two masks for this calculation. Maybe, there is another method/function for analyzing these energies, without manually calculated them (DEAB = EAB - EA - EB) from the potential energies generated from the molecular dynamics simulation. Could anyone help me with this question?
>>
>> Sincerely,
>>
>> Eduardo.
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Wed Mar 10 2021 - 00:30:02 PST
