AMBER Archive (2008)

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

From: Yong Duan (duan_at_ucdavis.edu)
Date: Fri Aug 22 2008 - 19:39:23 CDT

You may try to re-name the residues in one of two parameter sets into other
names and name the residues in the PDB accordingly. Then, you may be able to
load both UA and AA models and perhaps mix them. Hope this helps ...

yong

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
fatima.chami_at_durham.ac.uk
Sent: Friday, August 22, 2008 1:46 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: all & united atoms force field

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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