Re: Fw: Calculating Free Energy Change

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Apr 23 2004 - 11:08:12 CDT

Hi Shirley

The is the email I was talking about:

http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/0746.html

Changing conformations is equivalent to changing morphing from one residue
to another, so long as the change is only a "perturbation". For
example changing a proline conformation from cis to trans or vice versa
probably isn't a "perturbation" but my knowledge here is not great....

In your case lambda=0 is one confromation and lambda=1 is the final
conformation. Unless I have totally misunderstood your question.

Brian

On Thu, 22 Apr 2004, Shirley Hui wrote:

> Thank you for your reply.
> I searched the list for anything relating to what I wanted to do, but either I am not looking far back into the archive, or I really don't know what I am doing!
> This is the list I am searching:
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/
> Instead I am wondering if doing the following would do what I want.
> I was thinking of supplying NAMD with an fep file whereby the original conformation and the coordinates associated with that conformation are in the PDB-style file with -1.00 ('vanish'). In the same PDB-style fep file I would also have the coordinates for the perturbed conformation with 1.00 ('appear').
> Then I would run NAMD FEP calculations using this file.
> My thinking is that the original conformation is changing/perturbing to the perturbed conformation. Instead of residues vanishing or appearing, it's the same ones, but in different locations.
> Does this work - am I on the right track??
> I'm sorry, I was unable to find the tool that you are referring to below??
> Thanks for your insight,
> shirley
>
>
> >From: Brian Bennion <brian_at_youkai.llnl.gov>
> >To: Shirley Hui <shirleyhui_at_alumni.uwaterloo.ca>
> >Subject: Re: namd-l: Fw: Calculating Free Energy Change
> >Date: Thu, 22 Apr 2004 11:42:46 -0700 (PDT)
> >
> >Hi Shirley,
> >
> >From the user guide page you supplied it states that your problem can be
> >implemented in NAMD.
> >
> >Search this list for the description of a tool that creates the FEP
> >scripts based on two end points.
> >
> >Brian
> >
> >On Thu, 22 Apr 2004, Shirley Hui wrote:
> >
> > > I was wondering if anyone could clarify some things for me.
> > >
> > > NAMD's Free Energy Calculator was meant to calculate the free energy change between various perturbations of a molecule (the perturbations would be constrained).
> > > Does anyone know if it is possible to give NAMD two conformations of the same molecule and then calculate the free energy change between the two?? Basically I am perturbing a molecule myself and then I want to know the free energy change between the original conformation of the molecule and the perturbation I made. If not NAMD are there any other software that can do this?? If not, I guess I will have to implement my own and I know this is not a trivial task.
> > > Thanks for any insight, the examples on the web page on NAMD's Free Energy Calculator are a bit too in depth or detailed for me at the moment to fully understand.
> > > http://www.ks.uiuc.edu/Research/namd/current/ug/node33.html
> > > thanks,
> > > shirley
> > >
> >
> >*****************************************************************
> >**Brian Bennion, Ph.D. **
> >**Computational and Systems Biology Division **
> >**Biology and Biotechnology Research Program **
> >**Lawrence Livermore National Laboratory **
> >**P.O. Box 808, L-448 bennion1_at_llnl.gov **
> >**7000 East Avenue phone: (925) 422-5722 **
> >**Livermore, CA 94550 fax: (925) 424-6605 **
> >*****************************************************************
> >
>

*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
*****************************************************************

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