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From: Erdem Yeler <erdemyeler.gmail.com>

Date: Tue, 18 Feb 2020 13:19:47 +0300

Hi,

I want to simulate protein-ligand interaction in 70%water -30%ethanol

(percents for volume) For this;

1) Should assign "epsin" in input files? For example epsin = 80 #for water

2) Let's say I should assign new value to epsin. Can I use this formula :

(Prakongpan and Nagai, 1984; Chien, 1984; Dumanovic et al., 1992*) *

€mixture = a1€1+a2€2 (a is percent of volume and € is you know, epsilon :)

)

so for 70%water -30%ethanol

€=78*0.70 +24.3*0.3 = 61.89

or should I use (from this article: International Journal of Pharmaceutics

269 (2004) 353–360 A simple relationship between dielectric constant of

mixed solvents with solvent composition and temperature Abolghasem Jouyban)

this formula:

ln εm = φ1 ln ε1 + φ2 ln ε2 + φ1φ2 2 i=0 Ki(φ1 − φ2) i

3)is the method I am planning of doing this simulation (to assign epsin

value and to use the formula) wrong? if it is... what is the rightest way

to do it?

Thank you so much for your help by now

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http://lists.ambermd.org/mailman/listinfo/amber

Received on Tue Feb 18 2020 - 02:30:01 PST

Date: Tue, 18 Feb 2020 13:19:47 +0300

Hi,

I want to simulate protein-ligand interaction in 70%water -30%ethanol

(percents for volume) For this;

1) Should assign "epsin" in input files? For example epsin = 80 #for water

2) Let's say I should assign new value to epsin. Can I use this formula :

(Prakongpan and Nagai, 1984; Chien, 1984; Dumanovic et al., 1992*) *

€mixture = a1€1+a2€2 (a is percent of volume and € is you know, epsilon :)

)

so for 70%water -30%ethanol

€=78*0.70 +24.3*0.3 = 61.89

or should I use (from this article: International Journal of Pharmaceutics

269 (2004) 353–360 A simple relationship between dielectric constant of

mixed solvents with solvent composition and temperature Abolghasem Jouyban)

this formula:

ln εm = φ1 ln ε1 + φ2 ln ε2 + φ1φ2 2 i=0 Ki(φ1 − φ2) i

3)is the method I am planning of doing this simulation (to assign epsin

value and to use the formula) wrong? if it is... what is the rightest way

to do it?

Thank you so much for your help by now

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Tue Feb 18 2020 - 02:30:01 PST

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