Re: ABF calculation with TclForces script in the configuration file

From: govardhan reddy (greddy1_at_umd.edu)
Date: Fri Jan 16 2009 - 11:10:47 CST

Hello all,
Following upon my question, is using abf restraintList the best way
to apply harmonic restraint between two atoms in an ABF calculations.
For example if I want to restraint two atoms at a particular distance,
say 7.8 Ang in the ABF calculation, is this the way to do it
abf restraintList {
dist1 {dist {P1 1 CA} {P2 1 CA} 0.5 7.8}
}
Thanks
Greddy
On Jan 16, 2009, at 10:18 AM, govardhan reddy 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
>

***************************************************
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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