[Apbs-users] RE: More questions, sorry.

[Nathan B. <ba...@bi...>]

Hello --

I'm heading out of town for a meeting but I will Cc Todd Dolinsky who can
help you -- and the mailing list who should be able to offer general advice.

Thanks,

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: ds...@pi... 
> [mailto:ds...@pi...] 
> Sent: Tuesday, December 07, 2004 6:07 PM
> To: ba...@ch...
> Subject: More questions, sorry.
> 
> Nathan.
> 
> I'm sorry about messaging you so many times but I'm still 
> getting strange values on my EE (from 30 KCal to 220 KCal), I 
> attach one of my input files to see if you can help me about 
> this problem. Adittionaly I calculated Coulombic for every 
> PQR and scaled it by CE/2 because I'm using Dialec_Cons=2.
> 
> Thanks in advance.
> 
> Daniel Silva.
> 
> PS. I think you have a lot of work, so I will understant if 
> you have no time to answer my questions, but if possible, can 
> you direct me to readings about how to calculate this parameters?
> 
> 
> > Yes, definitely.  The calculations with homogeneous 
> dielectric should 
> > also have zero salt concentration.
> >
> > Thanks,
> >
> > Nathan
> >
> > ds...@pi... <ds...@pi...> 
> (11-26-2004
> > 13:20:53-0600):
> >>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
> >>>> >
> >>>>
> >>>> _______________________________________________
> >>>> apbs-users mailing list
> >>>> apb...@ch...
> >>>> http://cholla.wustl.edu/mailman/listinfo/apbs-users
> >>>>
> >>>
> >>>
> >>> _______________________________________________
> >>> apbs-users mailing list
> >>> apb...@ch...
> >>> http://cholla.wustl.edu/mailman/listinfo/apbs-users
> >>
> >>
> > End of message from ds...@pi....
> >
> > --
> > 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
> > PGP key:  http://cholla.wustl.edu/~baker/pubkey.asc
> > _______________________________________________
> > apbs-users mailing list
> > apb...@ch...
> > http://cholla.wustl.edu/mailman/listinfo/apbs-users
> 
> 
>