Hello!
Thanks a lot for your reply.
Yes, I want to use ONIOM QM/MM scheme, but with options that are not
available in G09. I have just started using Amber11 and I don't have
much experience. Could You, please, explain in few sentences how this
frcmod file with undeclared atoms is created?
Thanks,
Jura
Citiram Barbault Florent <florent.barbault.univ-paris-diderot.fr>:
> Hello,
>
> I am interested by this question... I never did that before but I
> think you can replace all atoms by undeclared names, such as YO for
> oxygen and YH1 YH2 for the two hydrogens. Then you create a new frcmod
> for these atoms (see xleap) with only the atomic partial charges. The
> problem you may have, is that all these atoms might collapse on your
> solute molecule if you minimize or run MD.
> If you want to use this to do ONIUM QM/MM simulations it would be more
> simple to use directly gaussian.
>
> Hope this will help you.
>
>
>
> On Tue, 12 Apr 2011 14:13:14 +0200
> Jurica Novak <jnovak.irb.hr> wrote:
>> Dear Amber user,
>>
>> Could anyone suggest me how to run Amber single point calculation in
>> a way
>> that atoms of solvent are represented only as a point charges (with
>> all
>> other interactions - bonding and nonbonding - turned off), while in
>> the same
>> time all interactions of solute atoms are accounted for?
>>
>> Thanks in advance,
>>
>> Jura
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> -------------------------------------------------
> Dr Florent Barbault
> Maitre de conferences / Assistant professor
>
> Universite Paris Diderot
> Laboratoire ITODYS
> 15 rue Jean de Baïf, bâtiment Lavoisier
> 75013 Paris FRANCE
> http://florentbarbault.wordpress.com/
> tel : (33) 01-57-27-88-50
> e-mail : florent.barbault.univ-paris-diderot.fr
> -------------------------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 12 2011 - 06:30:04 PDT
