yes but the original request was about glycoprotein so I thought I
would clarify for that request (not related to your work).
On Thu, Nov 20, 2008 at 11:21 AM, Barbault Florent
<florent.barbault.univ-paris-diderot.fr> wrote:
> Hello,
>
> In fact I did only carbohydrates-carbohdyrates interactions and I used ff03
> only for water....
>
> Regards
> Florent
>
> Le jeudi 20 novembre 2008, Carlos Simmerling a écrit :
>> I would actually recommend glycam and ff99SB. 99SB has been shown now
>> in several studies to perform better than ff03, and in my opinion the
>> charge model is consistent with glycam while that in ff03 may not be.
>> I'm not sure if anyone has tried the combination of ff03 and glycam,
>> whereas ff99SB uses the ff94 charge model and there are many studies
>> of this combination.
>>
>>
>>
>> On Thu, Nov 20, 2008 at 9:45 AM, Barbault Florent
>>
>> <florent.barbault.univ-paris-diderot.fr> wrote:
>> > Hello,
>> >
>> > I think you should use glycam and ff03. This works pretty well. Glycam
>> > deals with carbohydrates efficiently. Biomacromolecules and water are
>> > included in ff03 along with some ions
>> > Hope this will help.
>> >
>> > Regards
>> > Florent
>> >
>> > Le jeudi 20 novembre 2008, Wang,Ying a écrit :
>> >> Hi, dear all,
>> >> if i want to simulate a system including glycoprotein, protein,
>> >> polysacchride and ions. which forcefiled should i use? gaff?
>> >> Thanks a lot!
>> >>
>> >> -----------------------------------------------------------------------
>> >> The AMBER Mail Reflector
>> >> To post, send mail to amber.scripps.edu
>> >> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> >> to majordomo.scripps.edu
>> >
>> > --
>> >
>> > -------------------------------------------------
>> > Dr Florent Barbault
>> > Maitre de conferences
>> >
>> > NEW ADDRESS !!!
>> >
>> > Universite Paris Diderot
>> > Laboratoire ITODYS
>> > 15 rue Jean de Baïf, bâtiment Lavoisier
>> > 75013 Paris FRANCE
>> > http://www.itodys.univ-paris7.fr/
>> > tel : (33) 01-57-27-88-50
>> > e-mail : florent.barbault.univ-paris-diderot.fr
>> > -----------------------------------------------------------------------
>> > The AMBER Mail Reflector
>> > To post, send mail to amber.scripps.edu
>> > To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> > to majordomo.scripps.edu
>>
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber.scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo.scripps.edu
>
>
>
> --
>
> -------------------------------------------------
> Dr Florent Barbault
> Maitre de conferences
>
> NEW ADDRESS !!!
>
> Universite Paris Diderot
> Laboratoire ITODYS
> 15 rue Jean de Baïf, bâtiment Lavoisier
> 75013 Paris FRANCE
> http://www.itodys.univ-paris7.fr/
> tel : (33) 01-57-27-88-50
> e-mail : florent.barbault.univ-paris-diderot.fr
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Fri Dec 05 2008 - 16:10:10 PST
