Hello Marie,
Based on its structure, I would expect that the standard amino acids
bonded and Lennard-Jones parameters (i.e. parm14SB) would be able to model
a citrulline residue - or at least all terms should be present. What is
left are the partial atomic charges, which need to be done using the resp
protocol (ie. weighting factors of 0.0005 and 0.001) that was used for
AMBER's amino acid residues. If no one has done this, then you will
probably need to generate some conformations of a terminally capped
citrulline in order to generate conformations for the resp calculations.
Bests,
Karl
On Wed, Feb 10, 2016 at 3:13 PM, Marie Brut <marie.brut.laas.fr> wrote:
> Dear all,
>
> I need to introduce a citrulline residue in my protein and was wondering
> if someone had already calculated citrulline parameters ?
>
> Many thanks for your help,
>
> Marie
>
>
> Dr Marie Brut
> Associate Professor - University of Toulouse
> Atomic-scale Modeling of bio and bio-hybrid systems
>
> LAAS - CNRS
> Nano Engineering and System Integration Team
> 7 Avenue du Colonel Roche
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> 31031 Toulouse Cedex 4
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Received on Wed Feb 10 2016 - 07:00:04 PST
