Dear Dr. Anselm Horn,
Thank you for your response. I was in doubt about this calculation, since I was reading a paper about the linear interaction energy (LIE) :
N. Homeyer, H. Gohlke. FEW: A workflow tool for free energy calculations of ligand binding. J. Comput. Chem. 2013, 34, 11, 965-973.
In this paper, the authors presented some equations related with the binding free energies for multiple ligands using the LIE approach:
Einter = Etotal - Eligand - Erest (1)
<Einter,state> = 1/N Summation(i=1-n) Einter,state (2)
<DEinter> = <Einter,bound> - <Einter,free> (3)
DGbind = alpha<DEinter(vdW) + beta<DEinter(elec) + gama<DSASA> (4)
Thus, I was in doubt if the output generated from cpptraj (for the command lie) corresponded to the Einter (equation 1), DGbind (equation 2) or just the pairwise energy between two entities (for example EAB).
Thank you again for clarifying this question
Sincerely,
Eduardo.
________________________________
De: Dr. Anselm Horn <anselm.horn.fau.de>
Enviado: quarta-feira, 10 de março de 2021 05:15
Para: amber.ambermd.org <amber.ambermd.org>
Assunto: Re: [AMBER] Pair interaction energy
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 - 05:30:03 PST
