AMBER Archive (2008)

Subject: Re: AMBER: all & united atoms force field

From: fatima.chami_at_durham.ac.uk
Date: Fri Aug 22 2008 - 15:46:11 CDT

Quoting Ray Luo <rluo_at_uci.edu>:

>
> I understand your point in using AA and UA representations for
> different parts of your simulation system. However, I think this is
> pretty hard to do with leap. Dr. Wei Zhang, the current leap
> developer, may want to chip in on this ...
>

Thanks for the info.
I ll try to get in touch with Dr. Wei Zhang

best
fa.

> Also, you probably need to use ff03 for AA and ff03ua for UA because
> they are designed to be compatible.
>
> All the best,
> Ray
>
>
> 2008/8/22 <fatima.chami_at_durham.ac.uk>:
> > Quoting cgji <cgji_at_itcc.nju.edu.cn>:
> >
> >> hi,
> >>
> >> for all-atom force field ,you may try leaprc.ff99SB or leaprc.ff03
> >> for united-atom model ,you may try leaprc.ff03ua.
> >
> > Thanks for your reply
> > I already know about this...
> > what I dont know is to specify in leap the group of atoms that are to be
> > unified and those that are not ....in this way both force field are used
> > simultaneously
> >
> > I am not sure if this can be right to do
> >
> > best wishes
> > Fa
> >>
> >>
> >>
> >>
> >> Best Wishes,
> >> 2008-08-22
> >>
> >>
> >>
> >> cgji
> >>
> >>
> >>
> >> 发件人： fatima.chami
> >> 发送时间： 2008-08-22 06:07:11
> >> 收件人： amber
> >> 抄送：
> >> 主题： AMBER: all & united atoms force field
> >>
> >> Hello all,
> >> For a very large system i want to use both all and united atoms force
> field
> >> on
> >> different parts of the system
> >> is this possible in Amber (9 or 10)
> >> best wishes
> >> Fatima
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> >
> >
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