Re: [Apbs-users] apolar solvation energy

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

Hi Madhu --

The differences in format are described in more detail in the APBS  
documentation:  http://apbs.wustl.edu/MediaWiki/index.php/Flat-file_parameter_format

I agree that providing parameters for each atom/residue name (rather  
than type) is tedious; we've supplied some default parameters that  
should be useful for most applications with APBS in the tools/ 
conversion/param/vparam directory.

I hope this helps!

-- Nathan

On May 14, 2009, at 10:20 PM, Madhumalar Arumugam wrote:

> Hi Nathan,
>   I looked into the paper and tried to set the parameters for the  
> apolar
> calculation for prtn-pron interactions.
> The parameter file format in APBS is different from the parm file  
> read in
> AMBER.
>
> for example in APBS for water
> WAT     OW      0.000000        1.7683  0.6364
>
> in AMBER 94 dat file, without the charge field (includes only radii  
> and
> epsilon (kcal/mol)
>
> OW          1.7682  0.1521             TIP3P water model
>
>
> I don't understand how I can include residue name for every  
> aminoacid and
> corresponding charges, radii and epsilon?
> because in AMBER it is defined for atom types.
>
> many thanks
> Madhu
>
>
>> Hi Madhu --
>> We do not yet have any apolar parameters that have been specifically
>> optimized for protein-protein interactions.  We do have some that are
>> useful
>> for protein solvation forces with the AMBER force field; these are
>> described
>> in our earlier paper (http://dx.doi.org/10.1073/pnas.0600118103)  
>> and can
>> be
>> set with the
>> bconc<http://apbs.wustl.edu/MediaWiki/index.php/APOLAR_input_file_section#bconc 
>> >,
>> srad<http://apbs.wustl.edu/MediaWiki/index.php/APOLAR_input_file_section#srad 
>> >,
>> press<http://apbs.wustl.edu/MediaWiki/index.php/APOLAR_input_file_section#press 
>> >,
>> and
>> gamma<http://apbs.wustl.edu/MediaWiki/index.php/APOLAR_input_file_section#gamma 
>> >in
>>
>

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