Dear Sir,
Thanks very much for your explanation! I will try as you mentioned, and I will contact you if I have problems! Thanks!
All the best,
fancy
> -----原始邮件-----
> 发件人: steinbrt.rci.rutgers.edu
> 发送时间: 2010年4月13日 星期二
> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> 抄送:
> 主题: Re: [AMBER] How to prepare the two tolopogy files when doing TI calculation?
>
> Hi,
>
> there are many ways to do this and you should experiment a little to pick
> the one that suits you best. One option is to build your system in leap
> with both the initial and final states of the residue that changes (so two
> copies of it, at the same place), then delete each one of them to write
> your v0 and v1 prmtops.
>
> An alternative would be to make two pdbs which only differ in the group
> that changes and load them separately into leap. This leads to minor
> coordinate deviation because of center of mass imaging, but sander will
> correct for that.
>
> The only important thing is that the v0 and v1 prmtops have the atoms that
> do not change in the exact same order and (almost) same positions.
>
> Kind Regards,
>
> Thomas
>
>
> On Tue, April 13, 2010 8:29 am, fancy2012 wrote:
> > Dear amber users,
> > I want to do some TI calculation using GMX, and I have learned how to run
> > it from the web tutorial. But there is still a problem. I don't know how
> > to prepare the two topology files, which are initial and final states,
> > respectively. For example, molecule A to molecule B, while the two
> > molecules have only one different functional groups.
> >
> > Could somebody give me some suggestion on it? Any response will be highly
> > appreciated! Thanks!
> >
> > All the best,
> > fancy
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> Dr. Thomas Steinbrecher
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Tue Apr 13 2010 - 06:00:05 PDT
