Thanks we will try that too...
Another thing we've done is optimized and calculated the energy and charges
of the Ser-PPP resiude in Gamess.
But then how do I make the mol2 file and frcmod files?
To have closed shells I added extra hydrogens to the Ser where it would be
joined with the other amino acids.
David
On Thu, Jun 30, 2011 at 9:07 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear David,
>
> You could try R.E.D. Server; we just released a new feature about
> fragments related to amino acids. You provide a single input for your
> new dipeptide to R.E.D. Server and FF libraries with RESP or ESP
> charges (in the mol2 file format) are automatically generated for the
> dipeptide + its three corresponding fragments (central, N-termnal &
> C-terminal amino acid fragments). No need anymore to add information
> about specific constraints during the fitting step, R.E.D. Server does
> directly the job.
> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
> versus http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
>
> regards, Francois
>
>
> Quoting David Cantu <cantudav.gmail.com>:
>
> > 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.
> >
> > Thank you,
> >
> > David
>
>
>
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Received on Thu Jun 30 2011 - 11:00:03 PDT
