RE: [Apbs-users] Sorry I send this mail yesterday but I forget Subject: Help about EE calculations

[<ds...@pi...>]

Sorry again, but I'm still getting strange values, so question is:

Are salts concentrations important to this calculations?.

Thanks
Daniel Silva


> The most common error in these types of calculations arises when the
> "vacuum" calculation has an inhomogeneous dielectric coefficient.  What
> values of the solvent and solute dielectric coefficients are you using
> for the "vacuum" calculations?  These should be the same...
>
> Suppose your protein has a dielectric coefficient of 12 and exists in
> different conformations in the apo and holo states.  Then you will need
> to carry out the following calculations:
>
> 1) "Solvation energy" of unligated protein in apo conformation:
>   a) Calculation with inhomogeneous dielectric (protein = 12, solvent =
>   80) b) Calculation with homogeneous dielectric (protein = 12, solvent
>   = 12)
> 2) "Solvation energy" of unligated protein in holo conformation:
>   a) Calculation with inhomogeneous dielectric (protein = 12, solvent =
>   80) b) Calculation with homogeneous dielectric (protein = 12, solvent
>   = 12)
> 3) "Solvation energy" of ligated protein in holo conformation:
>   a) Calculation with inhomogeneous dielectric (protein = 12, solvent =
>   80) b) Calculation with homogeneous dielectric (protein = 12, solvent
>   = 12)
> 4) "Solvation energy" of ligand in holo conformation:
>   a) Calculation with inhomogeneous dielectric (ligand = 12, solvent =
>   80) b) Calculation with homogeneous dielectric (ligand = 12, solvent
>   = 12)
> 5) Coulombic energy of unligated protein in apo conformation with
> dielectric of 12
> 6) Coulombic energy of unligated protein in holo conformation with
> dielectric of 12
> 7) Coulombic energy of ligated protein in holo conformation with
> dielectric of 12
> 8) Coulombic energy of ligand in holo conformation with dielectric of
> 12
>
> You will then have the quantities that can be assembled via a free
> energy cycle to give you your binding energy.
>
> Good luck!
>
> -- Nathan
>
> --
> Nathan A. Baker, Assistant Professor
> Washington University in St. Louis School of Medicine
> Dept. of Biochemistry and Molecular Biophysics
> Center for Computational Biology
> 700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110
> Phone:  (314) 362-2040, Fax:  (314) 362-0234
> URL:  http://www.biochem.wustl.edu/~baker
>
>> -----Original Message-----
>> From: apb...@ch...
>> [mailto:apb...@ch...] On Behalf Of
>> Daniel Adriano Silva Manzano
>> Sent: Tuesday, November 23, 2004 3:36 PM
>> To: ba...@bi...
>> Cc: vk...@ma...; apb...@ch...; to...@cc...
>> Subject: [Apbs-users] Sorry I send this mail yesterday but I
>> forget Subject: Help about EE calculations
>>
>>
>>
>> On Mon, 22 Nov 2004 ds...@pi... wrote:
>>
>> > Nathan Baker, Todd, and APBS users:
>> >
>> > I'm sorry to make this kind of questions but actually I
>> cannot figure
>> > how to solve this.
>> >
>> > As in the tutorial I have a protein that interact with a
>> ligand so I
>> > made my electrostatic calculations on complex protein and
>> ligand with
>> > same grid and conditions for every one, then:
>> >
>> > deltaGelec (dGe)= TotalEE_complex -  TotalEE_protein -
>> TotalEE_ligand
>> >
>> > but then I think: if in the tutorial the electrostatic energy of a
>> > protein
>> > is:
>> > electrostatic energy (EE)= TotalEE _vacuum_protein -
>> TotalEE _protein
>> >
>> > then I can make:
>> >
>> > dGe = EE_complex -   EE_protein -  EE_ligand
>> >
>> > but I obtain totally different results as:
>> >
>> > deltaGelec (dGe)= TotalEE_complex -  TotalEE_protein -
>> TotalEE_ligand
>> > =
>> > 6.44 kJ/mol
>> > dGElectrostaticEnergy (EE)= TotalEE _vacuum_protein -
>> TotalEE _protein
>> >  = -287.3 -  6.44 = - 293
>> >
>> > So sorry again, but question:
>> > why calculus give different results?.
>> >
>> >
>> > This is important to me, because I'm calculating
>> electrostatic change
>> > of a protein that in the un-liganded state haves a open
>> state and in
>> > liganded state haves a closed state with ligand inside,
>> what made no
>> > usefull first method of dGe calculation
>> >
>> > Thanks
>> >
>> > Daniel Silva.
>> >
>> >
>> >
>> > _______________________________________________
>> > apbs-users mailing list
>> > apb...@ch...
>> > http://cholla.wustl.edu/mailman/listinfo/apbs-users
>> >
>>
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