Re: [AMBER] InVacuoWithDielc

Date: Tue, 02 Aug 2016 07:32:58 +0000

Thank you for your answer,

I tested different values for the variables involved in igb=6 option:

1. With igb = 6, variable dielc do nothing .....

2. But with igb=6, variable intdiel act as dielectric constant for electrostatic calculations.
Using this variable both approximations produce the same results.

De: David A Case []
Enviado: sábado, 30 de julio de 2016 16:51
Para: AMBER Mailing List
Asunto: Re: [AMBER] InVacuoWithDielc

On Fri, Jul 29, 2016, JAIME RUBIO MARTINEZ wrote:
> I am trying to study a peptide in vacuum, but with a dielectric constant
> (different solvents )
> However the two options that I tested produce different results .

dielc is ignored when igb>0. (You should run some test calculations to
confirm/refute this.)

> What is the right one ?

Neither. First, because different solvents differ in more than just the
dielectric. Second, because the peptide/protein atomic charges for Amber
have been developed for water solvation. These charges would not be the same
in different solvents.

The calculations you propose should only be used for very qualitiative

...good luck....dac

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