Re: ABF calculation with TclForces script in the configuration file

From: Jerome Henin (heninj_at_gmail.com)
Date: Fri Jan 16 2009 - 11:20:27 CST

Hi Greddy,
The boundary condition is: you cannot use both ABF and a custom
TclForces script in NAMD 2.6.

Now, depending on which type of restraints you want to apply, some
things are possible. If you want to keep parts of the protein in
place, then harmonic positional restraints ("constraints", in
NAMD-speak - boy, do I hate that) are the way to go. Distance
restraints and a few others can be applied from within the ABF module.
Finally, the "free energy of conformational change" function, also
known as conformational FEP, can do restraints - if you can figure it
out, that is.

Best,
Jerome

On Fri, Jan 16, 2009 at 10:18 AM, govardhan reddy <greddy1_at_umd.edu> wrote:
> Hello,
>
> I am interested in performing an ABF calculation. But I need to apply
> harmonic restraints on parts of the protein to keep it stable. I have a TCL
> script in the configuration file which does that. But if I need to perform
> the ABF calculation which also uses the TclForces and TclForcesScript, I
> cannot call the TclForces command from the configuration file to apply the
> harmonic restraints on the protein. What is the best way to perform ABF
> calculation and at the same time apply harmonic constraint on the protein to
> keep it stable.
>
> Thanks
> Greddy
>
>
> ***************************************************
> Govardhan Reddy
> Research Associate
> Institute for Physical Science and Technology
> University of Maryland-College Park
> College Park, MD - 20742
> Phone: +1-301-405-4822
> Fax: +1-301-314-9404
>
>

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