Dear Karl,
Thank you so much for your detailed answer, it will help a lot.
I will try to follow the steps you describe…
All the best,
Marie
> Le 10 févr. 2016 à 15:36, Karl Kirschner <k.n.kirschner.gmail.com> a écrit :
>
> 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 <mailto: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
>> BP 54200
>> 31031 Toulouse Cedex 4
>> Phone. : (+33) 5 61 33 63 04
>> Fax : (+33) 5 61 33 62 08
>> http://www.laas.fr/N2IS/ <http://www.laas.fr/N2IS/> <http://www.laas.fr/N2IS/ <http://www.laas.fr/N2IS/>>
>> https://homepages.laas.fr/mbrut/ <https://homepages.laas.fr/mbrut/> <https://homepages.laas.fr/mbrut/drupal/ <https://homepages.laas.fr/mbrut/drupal/>>
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Received on Wed Feb 10 2016 - 12:30:04 PST
