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 - 07:30:03 PDT
