[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 RUN OPTIONS
>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 
matter
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.

Berk.

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