peptid bond omega, problems with settings?

From: Hua Wong (
Date: Thu Apr 15 2004 - 02:27:38 CDT

I have a problem with setting up minimization.
I start up with a protein with averagely good absolute deviation of omega torsion (used Procheck).
And after using NAMD to minimize it, I end up with a minimized model but a rather awful lot of residues with abnormal deviation of omega torsion (Omega absolute mean deviation between 14 and 16)

Am I doing something wrong or is it normal? Is there a setting I forgot?

Here I join the .namd file I use to run NAMD.

numsteps 10000
timestep 1

coordinates fooprot.pdb
structure fooprot.psf
parameters par_all22_prot.inp
paraTypeCharmm on

minimization on

cutoff 20.0
pairlistdist 20.5
switching off

exclude 1-4

outputname fooprot_out

IMDon on
IMDfreq 1
IMDport 3111

temperature 300
minimize 400

run 200000

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