Hi Ben,
Do I use reduce and antechamber with the entire PDB? How do I choose only
the 1 residue (combined Ser-PPP) for antechamber?
David
On Wed, Jun 29, 2011 at 12:50 PM, Ben Roberts <ben.roberts.geek.nz> wrote:
> Hi David,
>
> On 29/6/2011, at 1:38 p.m., David Cantu wrote:
>
> > Dear Amber Users/Developers,
> >
> > We have a protein, which has a phosphopantethiene group (call it resiude
> > PPP) attached to a serine (through a P-O bond). We tried loading this
> > Ser-PPP residue into antechamber, but failed.
> >
> > If we load the PPP by itself, using Antechamber, a hydrogen will take the
> > place of the P-O bond. We cannot load it with an open valence. Any ideas
> no
> > how to load both the PPP and Ser as a non-standard resiude? We need the
> > correct parameters for the P-O bond.
>
> About the only thing I can suggest is to combine the PPP and serine into a
> single residue, with its own three-letter residue code and residue number.
> Then,
> antechamber should handle it without any problems.
>
> Good luck!
>
> Ben
>
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Received on Wed Jun 29 2011 - 13:00:03 PDT
