how to use constraints properly

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Thu Mar 19 2009 - 13:38:24 CDT

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

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