Subject: Re: [modeller_usage] absolute position restraints
From: Modeller Caretaker <>
Date: Tue, 17 May 2005 12:39:10 -0700
Cc:
Frank Böckler wrote:
I'm trying to keep some part (ligand) fixed in space using the restraint
features 9, 10 and 11 and the restraint type 34.
Unfortunately, I was not quite successful with this approach (outlined
below).
Can anybody give me an advice, how to proceed correctly (correct syntax
for the restraints, other approach giving the same result, ...)?
If you don't want part of your system to move at all, you can just
deselect it. Modeller only optimizes selected atoms. See
MODELLER5 VERSION: MODELLER FORMAT
R 3 1 9 34 1 2 0 1936 46.483 0.0
My idea was to constrain the x, y or z coordinate (feature 9, 10, 11) of
the ligand with a harmonic potential (3) written into restraint type 34
and applied on 1 atom (using 2 parameters: the coordinate and the standard
deviation). I've used both 0.0 and higher values as standard deviations to
fix the atom position absolutely or to allow some movement, however both
was unsuccessful. Perhaps the whole syntax is false???
Your syntax looks fine, but it won't work with a stdev of 0. If it
doesn't work with a non-zero stdev either, then I'm not sure exactly
what's wrong. Send me your input files and I'll take a look.