[gmx-users] pull code and constrain distance--help-please

John Simms JXS818 at bham.ac.uk
Tue Mar 22 16:16:44 CET 2005

Hi All,
I am a bit stuck, i have a docked (autodock) ligand in a binding pocket and would like to do a small series of SA steps. I have used the pull code in a effort to keep the ligand in approximately the same position (ie allow motion in the x, y direction but keep the z direction distance constrainted), but the ligand keeps floating out of the binding pocket. below is my pull-in.ppa file, what am i doing wrong
verbose                  = no
Skip steps               = 1
runtype                  = constraint
group_1                  = lig
reference_group          = Backbone
reftype                  = com
reflag                   = 1
pulldim                  = N N N
r                        = 0
rc                       = 0
update                   = 1
constraint_direction     = 0.0 0.0 1.0
Also the constraint_direction bit, what do the numbers represent. are they multiplication factors? looking through the list different people have used a range of values bewteen 0 and 1.
If you can help i would be very grateful
Many Thanks in advance

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