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".
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
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > 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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Received on Tue Aug 17 2010 - 09:30:06 PDT
