Re: how to use constraints properly

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Thu Mar 19 2009 - 13:53:09 CDT

For the type of distance you're talking about do you really require a
hard constraint? I would just use tclforces to harmonically restrain
the distance between the two residues. You can crank up the force
constant to decrease the fluctuations down to whatever level you want
assuming that you don't compromise the integrator. Depending on how
far apart these residues are to begin with, I'd be careful about how
you increase/decrease the distance so you don't blow your system up.

Josh

On Mar 19, 2009, at 11:38 AM, Roman Petrenko wrote:

> Hello all,
> i have some initial protein structure, which i'd like to modify in
> such a way that the distance between residues 1 and 30 is exactly 90
> A. First, i tried free energy, but it fails. I actually don't intend
> to evaluate free energy difference, i just thought this would be the
> easiest way to do. Then, i used "constraints on" option and also got
> an error from RATTLE algorithm. Only applying a constant force (or
> using SMD) worked fine, but it is inconvenient since one have to
> adjust the number of steps for every initial structure.
>
>
> Here is relevant part of the configuration file:
>
> --------------------------------------------
> freeEnergy on
> freeEnergyConfig {
> urestraint {
>
> dist (SEG0, 1, CA) (SEG0, 30, CA) kf=20 ref=90
> }
> pmf {
> task = stop
> time = 100 ps
> }
> }
> structure prot.psf
> coordinates prot.pdb
> set temperature 310.0
> set run_steps 50001
> ---------------------------------------------
>
>
>
>
> which gives the following error:
>
>
> Info: FREE ENERGY PERTURBATION CONFIG
> Info: ***********************************
>
> urestraint {
> dist (SEG0, 1, CA) (SEG0, 30, CA) kf=20 ref=90
> }
> pmf {
> task = stop
> time = 100 ps
> }
>
> Info: ***********************************
> FreeEnergy: Not enough steps to complete pfm & mcti blocks
> FreeEnergy: Num Steps Needed = 50001
> FreeEnergy: Num Steps Requested = 0
> FATAL ERROR: FreeEnergy: Fatal Run-Time Error
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: FreeEnergy: Fatal Run-Time Error
>
>
>
>
> --
> Roman Petrenko
> Physics Department
> University of Cincinnati
>

------------------------------------------------------------------------
------------------------------
Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley http://nature.berkeley.edu/
~jadelman
Berkeley, CA 94720 USA jadelman_at_berkeley.edu
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