Re: [Apbs-users] Highly positive solvation energy

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

Hi David --

Your positive energy is because the current energy calculation is  
evaluating the transfer from a high dielectric environment (80) to a  
low dielectric (2).  If you reverse the order of calculations in the  
print statement (or just change the sign of the answer), you should  
have the desired output.

Thanks,

Nathan

On Aug 6, 2009, at 4:31 PM, Davide Mercadante wrote:

> Dear Dr. Baker,
>
> thanks for the quick reply.
> As you requested I attach in this mail the files .in and .pqr that I  
> used to do the calculations.
>
> Thank you again for any help.
>
> Cheers,
> Davide
>
> 2009/8/7 Nathan Baker <ba...@bi...>
> Hello --
>
> I'm sorry but it's very difficult to answer your question without  
> more information.  Could you please attached the APBS input file  
> and, ideally, the PQR file as well?
>
> Thanks,
>
> Nathan
>
>
> On Aug 5, 2009, at 11:16 PM, Davide Mercadante wrote:
>
> Dear Dr. Baker,
>
> I performed APBS calculations on a dimer of 162aa residues per  
> monomer to calculate the desolvation effect. I had the .in file from  
> the pdb2pqr command line software after the creation of the .pqr  
> file. However, I have compared my input file with one of those given  
> in the APBS tutorial and some of the parameters are different, for  
> example the "gamma" parameters doesn't exist in my input file.
>
> I tried to insert it but I have a warning message saying to read the  
> new documentation for apolar calculations.
> Please, can you address me to the web page where I can find this  
> documentation?
>
> In addition, I have a question about the solvation energy. After the  
> calculation I get as solvation energy the following:
>
> PRINT STATEMENTS
>
> print energy 2 - 1 end
>  Local net energy (PE 0) = 4.129643953660E+04 kJ/mol
>  Global net ELEC energy = 4.129643953660E+04 kJ/mol
>
> Why I get so high positive energetic value?
>
> Thanks in advance for any explanation.
>
> Cheers,
> David
>
> —
> Associate Professor, Dept. of Biochemistry and Molecular Biophysics
> Director, Computational and Molecular Biophysics Graduate Program
> Center for Computational Biology, Washington University in St. Louis
> Web: http://bakergroup.wustl.edu/
>
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> <1BEB_G64D2_noW.in><1BEB_G64D2_noW.pqr>

—
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Director, Computational and Molecular Biophysics Graduate Program
Center for Computational Biology, Washington University in St. Louis
Web: http://bakergroup.wustl.edu/