Hi Guys --
I think that's a fair expectation with the --assign-only flag;
otherwise, I think that PDB2PQR should require the user to specify
N/C/both-terminal residue status.
Thanks,
Nathan
On 9/19/07, Robert Konecny <rok@uc...> wrote:
> Hi Todd,
>
> yes, exactly. I was expecting that pdb2pqr would just assign radius/charge
> per atom, not trying to be smart about residue type (N-terminal vs
> C-terminal). Just simply a lookup in atom-residue table.
>
> thanks,
>
> r.
>
>
> On Wed, Sep 19, 2007 at 10:48:33AM -0400, Todd Dolinsky wrote:
> > The quick answer is that for single residues PDB2PQR doesn't know
> > whether to make it the residue N-terminal, C-terminal, both, or
> > neither. The "both" choice is the one that PDB2PQR can't support in
> > some forcefields (i.e. AMBER) since those forcefields are not based on
> > patching - there's no way to make things simultaneously N and C
> > terminal.
> >
> > If we'd like to assign neither an N or C-terminus to the residue, then
> > there's no reason we can't support it. Is this the desired case?
> > What do you believe should be the expected behavior?
> >
> > Thanks -
> >
> > Todd
> >
> > On 9/18/07, Robert Konecny <rok@uc...> wrote:
> > >
> > > Hi Nathan,
> > >
> > > On Tue, Sep 18, 2007 at 07:29:02PM -0500, Nathan Baker wrote:
> > > > Hi Robert --
> > > >
> > > > > running pdb2pqr on a pdb file with a single residue I get this:
> > > > >
> > > > > /opt/apbs-0.5.0/pdb2pqr/pdb2pqr.py --assign-only --ff=amber
arg.pdb arg.pqr
> > > >
> > > > ...
> > > >
> > > > > ValueError: Unable to support amino acid chains of only one
residue (ARG 1)
> > > >
> > > > Well, at least it gave you a comprehensible error! Actually, this
is
> > > > likely a bug; I'll Cc Todd to make sure but will also go ahead and
> > > > file a bug report since this should work.
> > > >
> > > > > Why is this not working? Even with the '--assing-only' option?
> > > >
> > > > However, I'm guessing that the '--assing-only' option didn't work
> > > > because PDB2PQR took offense to the language. :)
> > >
> > > hehe, that's a good one :) But the bug is still there even when I'm more
> > > polite to pdb2pqr and use the correct option.
> > >
> > > thanks!
> > >
> > > r.
> > >
> > >
> >
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--
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/
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