On Tue, Aug 17, 2010 at 12:04 PM, Daniel Sindhikara <sindhikara.gmail.com>wrote:
> Catherine,
> It seems like these are more general science questions not related
> directly to "how to use AMBER" but If you are
> trying to identify pathways, the first method I would recommend that AMBER
> has to offer is nudged elastic band (NEB). Which is specifically designed
> to
> find pathways. The methods Jason mentioned are used primarily to calculate
> PMF once an ideal pathway has
> been found. I would recommend reading the many articles referenced in the
> AMBER manual regarding "NEB".
>
I threw NEB in there at the end :). However, as I understand it, NEB won't
really give a PMF in the sense that it won't be a free energy path along
that coordinate. I think you need to further use umbrella sampling at
various points along that coordinate in order to actually generate the PMF
after the NEB simulation. Am I right?
All the best,
Jason
> However, if it is a relatively simple pathway, of course PMF methods are
> the
> way to go.
>
> --Dan
>
> On Wed, Aug 18, 2010 at 12:36 AM, Catein Catherine
> <askamber23.hotmail.com>wrote:
>
> >
> > Thank you Jason,
> >
> >
> >
> > How about if I was doing this with umbrella sampling?
> >
> >
> >
> > Can I identify the most important drug dissociation pathway using
> umbrella
> > sampling? When I find different results since I used different atoms to
> > define the distance restraint?
> >
> >
> >
> > Best regards with thanks,
> >
> >
> >
> > Catherine.
> >
> > > Date: Tue, 17 Aug 2010 08:56:29 -0400
> > > From: jason.swails.gmail.com
> > > To: amber.ambermd.org
> > > Subject: Re: [AMBER] How to find the most important drug dissociation
> > pathway theoretically? PMF?
> > >
> > > Hello,
> > >
> > > How are you constructing the PMF? Are you using SMD and calculating the
> > PMF
> > > with the Jarzynski equation? Are you using umbrella sampling? If you
> are
> > > using SMD with Jarzynski averaging, you should include every single
> > > trajectory in your average to get the total PMF. You can find likely
> the
> > > "best" pathway, or the one that corresponds closest to the PMF, by
> > comparing
> > > the potential energy surface of each simulation with the average PMF
> > > obtained from averaging all of them, and whichever one follows that
> curve
> > > closest will probably be a good choice.
> > >
> > > Hope this helps,
> > > Jason
> > >
> > > On Tue, Aug 17, 2010 at 7:00 AM, Catein Catherine <
> > askamber23.hotmail.com>wrote:
> > >
> > > >
> > > > Dear All,
> > > >
> > > >
> > > >
> > > > I would like to stuy the drug dissociation pathway from a receptor.
> > > >
> > > >
> > > >
> > > > I tried to use PMF to discript the distance between the drug and the
> > active
> > > > site. I noted that the path is sensitive to the atoms used to define
> > the
> > > > distance restraint.
> > > >
> > > >
> > > >
> > > > If I want to chose the most important drug dissociation pathway for
> > further
> > > > discussion, is the one with the lowestest energy should be used? If
> > not,
> > > > what is the requirement should be used to chose the right pathway?
> > > >
> > > >
> > > >
> > > > best regards,
> > > >
> > > >
> > > >
> > > > Cat
> > > >
> > > > _______________________________________________
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> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Graduate Student
> > > 352-392-4032
> > > _______________________________________________
> > > 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
> >
>
>
>
> --
> Dr. Daniel J. Sindhikara
> Institute for Molecular Science
> E-mail: sindhikara.gmail.com
> Website: http://sites.google.com/site/dansindhikara/
> --
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Aug 17 2010 - 11:00:07 PDT
