[gmx-users] position restraints

[Shima Arasteh]

Hi Dear Justin


First of all, I request you that not to shout at me! I am so sorry to ask you questions about position restraints again!

I
 know I have sent you such emails before, and you suggested me to read 
include file mechanism in web site. I did this and also read some emails
 in forum. But I think I have problems with include mechanism. Again I 
got into the trouble about position restraining:

As you told me -DPOSRES will not trigger #ifdef POSRE or #ifdef DPOSRES.

I
 have a system of POPC/ions/waters and a double chain protein inserted 
in POPC bilayer. I put restraints on P headgroups and protein. I added 
the define line to the mdp file as follow:
define        = -DPOSRES_LIPID -DPOSRES

Then added the itp files to my top as follow:

; Include chain topologies
#include "topol_Protein_chain_A.itp"
#ifdef POSRE
#include "protein_chain_A_posre.itp"
#endif
#include "topol_Protein_chain_B.itp"
#ifdef POSRE
#include "protein_chain_B_posre.itp"
#endif

; Include POPC chain topology
#include "popc.itp"
#ifdef POSRES_LIPID
#include "lipid_posre.itp"
#endif


But when I run the grompp with -pp flag, I see that restraints on chain_B are not included!

Then
 I changed the numbering in protein_chain_B_posre.itp to what they are 
in their original itp file, generated earlier by pdb2gmx. Do you agree 
that it is the problem which I encountered with? 
Now when I run grompp I see the restraints after each chains with the same numbering.


Sincerely,
Shima

 
Sincerely,
Shima


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Tuesday, March 26, 2013 12:02 AM
Subject: Re: [gmx-users] position restraints



On 3/25/13 3:25 PM, Shima Arasteh wrote:
> Dear Justin,
> 
> As I got, I need to edit the lipid_posre.itp file. To do so, I need to change numbering of position restraining in lipid_posre.itp file to what they are in their original itp file: In my case popc.itp file.
> Am I right?
> 

More or less, but for the sake of clarity, let me explain this fully so you can hopefully arrive at a resolution quickly.  Say I have a system of arbitrary molecules that have 4 atoms each.  Position restraints only work per [moleculetype], so using genrestr is somewhat dangerous unless you are working with a coordinate file or suitable index file that only specifies a single molecule.  Otherwise, the selection is rather ham-handed and actually gives you a nonfunctional .itp file (hence the WARNING in the help description). Therefore, I can only use atom numbers 1, 2, 3, and 4 in my [position_restraints] directive.  Anything above 4 (i.e. based on selecting multiple molecules in genrestr) triggers a fatal error.

What then happens is that grompp reads those atoms, and every time it encounters those atom numbers within the [moleculetype] (irrespective of how many times that molecule appears), restraints are applied as specified.

So, if you want to restrain only P atoms of every POPC molecule, you basically need a one-line .itp file.  If, for instance, P is atom number 8:

[ position_restraints ]
   8   1   0    0    1000

That will restrain all P atoms (every time they occur, as grompp finds them throughout the coordinate file) in the z-dimension only.  Hopefully that all makes sense and this experience has been educational as far as how these things work.

-Justin

-- ========================================

Justin A. Lemkul, Ph.D.
Research Scientist
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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