abdullah ahmed wrote:
Thank you for your reply,
I have been using [ position_restraints ], I do not know why it came out
that way in the mail.
I agree with you, the problem probably comes from the position the code
lies in inside the .top file. I put it at the end of the file because I
thought that was the way it was supposed to be done. Perhaps this is
incorrect.
That is incorrect. The position restraints must belong to the [moleculetype] of
the species to be restrained. Once you #include a new molecule, you start a new
[moleculetype] entry and the position restraints belong to it. Putting it at
the very end of a file probably has no effect whatsoever on any of the species
in your system.
-Justin
The final lines of the .top file are:
Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
Protein
[ molecules ]
; Compound #mols
Protein_A 1
[ position_restraints ]
2 1 1000 0 1000 ;
3 1 1000 0 1000 ;
4 1 1000 0 1000 ;
5 1 1000 0 1000 ;
6 1 1000 0 1000 ;
7 1 1000 0 1000 ;
8 1 1000 0 1000 ;
9 1 1000 0 1000 ;
> Date: Thu, 3 Jun 2010 09:00:36 -0400
> From: [email protected]
> To: [email protected]
> Subject: Re: [gmx-users] position restraints
>
>
>
> abdullah ahmed wrote:
> > Hello,
> >
> > I would like to restrain my molecule to a specific position in
space. I
> > would like for certain atoms to lie on the y-axis. To do this I used
> > the following code/lines in my .top file:
> >
> > [ position restraints ]
>
> This is an incorrect directive. It should be position_restraints.
>
> > 2 1 1000 0 1000 ;
> > 3 1 1000 0 1000 ;
> > 4 1 1000 0 1000 ;
> > 5 1 1000 0 1000 ;
> > 6 1 1000 0 1000 ;
> > 7 1 1000 0 1000 ;
> > 8 1 1000 0 1000 ;
> > 9 1 1000 0 1000 ;
> >
> > Unfortunately, after minimization my file contained the molecule in
the
> > same position as when the restraints were not applied.
> >
> > Does anyone know what I am doing wrong?
> >
>
> Perhaps the directive name is an issue, although I think grompp
should have
> raised a warning of some sort. Otherwise, is this block within the
appropriate
> [moleculetype] in the topology? Is it under control of an #ifdef
block that you
> haven't invoked in the .mdp file?
>
> -Justin
>
> > Thanks in advance,
> > Abdullah
> >
> >
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> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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