From: MW Van der Kamp, School of Chemistry (Marc.VanderKamp_at_bristol.ac.uk)
Date: Fri Oct 20 2006 - 07:24:04 CDT
Hello,
I'm trying to restrain the distance between sets of two (unconnected) atoms
to a maximum distance (3 Ang). In my starting structure, distances are
smaller then 3 Ang. If I run an unrestrained minimization, distances become
larger than 3 Ang.
However, when I try to apply restraints, I get exactly the same result!
I tried to use commands from the 'Free energy of conformational change
calculations' section of the user guide
(<http://www.ks.uiuc.edu/Research/namd/2.6/ug/node34.html>)
This is my addition to my config file:
freeEnergy on
freeEnergyConfig {
urestraint {
dist bound (MAPP, 1, O1) (PROA, 233, CE1) kf=50 hi=3
dist bound (MAPP, 1, O2) (PROA, 233, CE2) kf=50 hi=3
}}
Which seems to be read in correctly (output):
Info: FREE ENERGY PERTURBATION CONFIG
Info: ***********************************
urestraint {
dist bound (MAPP, 1, O1) (PROA, 233, CE1) kf=50 hi=3
dist bound (MAPP, 1, O2) (PROA, 233, CE2) kf=50 hi=3
}
Info: ***********************************
The resulting minimization however is exactly the same as the one without
restraints (both energy values and coordinates). So my restraints do not
come into effect.
Does anyone know what can be going wrong?
Many thanks,
Marc
---------------------------------------------------
Marc van der Kamp, PhD-student
School of Chemistry, Research group of Dr. Adrian Mulholland
University of Bristol
E-mail: Marc.vanderKamp_at_bristol.ac.uk
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