Re: [Apbs-users] more iAPBS/CHARMM problems

[Hannes L. <Han...@st...>]

Hi Nathan,

On Wed, 24 Mar 2010 10:52:45 -0500
Nathan Baker <ba...@bi...> wrote:

> Hi Hannes --
> 
> > Somewhat offtopic, I was wondering if there is a modified
> > dat/CHARMM.DAT available for pdb2pqr with Benoit Roux's set of
> > radii.
> 
> No, but they could be added if there was a general need.  Which set of
> radii are you referring to?

http://thallium.bsd.uchicago.edu/RouxLab/downloads/charmm/pbeq/radius.str

Also part of any (recent?) CHARMM distribution and also iAPBS.

Unfortunately, that's just basically a CHARMM script that internally
modifies the radii from the PSF file, I think.  I'll have to try if I
can extract these from a newly created PSF (after reading radius.str).
Didn't think about this earlier...  Then I could just create a new .DAT
file using the existing one as template, at least for the amino acid
residues.

Thanks a lot,
Hannes.