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

Berk Hess gmx3 at hotmail.com
Tue Mar 22 17:57:23 CET 2005

>From: "John Simms" <JXS818 at bham.ac.uk>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: <gmx-users at gromacs.org>
>Subject: [gmx-users] pull code and constrain distance--help-please
>Date: Tue, 22 Mar 2005 15:16:44 -0000
>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.

The problem is pulldim, this should be N N Y, now your constraint works in 
no dimensions.
There are many, equivalent options for this case.
With N N Y you can also use direction 0 0 0
With Y Y Y you should use direction 0 0 1, although the magnitude does not 
as is written in the new pull manual which I posted some time ago.

You reference group is not completely correct, this should be protein,
as you probably have constraints turned on, but for your system this
is probably irrelevant.


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