chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue Jul 28 04:24:25 CEST 2009

Sounds to me like you have a 52 atom lipid and have a posre.itp file  
with more than 52 atoms (or referencing atom numbers greater than 52).  
What one usually does is has a somelipid.itp file that, upon some .mdp  
define, includes a someposre.itp file that looks like this:

[ position_restraints ]
; atom  type      fx      fy      fz
      8     1  1000  1000  1000

where for a 52 atom lipid I assume that you are using Berger lipids  
and atom 8 is the Phosphorous.

On the other hand, if you have a .itp file that specifies N-lipids,  
then you would need lots of [ position_restraints ]. Caution: this is  
not the best way to go as you will need to modify many files every  
time you set up a new bilayer.

As an analogy, look at the way that the SOL (tip4p in this case) posre  
is applied in a generic .top out of pdb2gmx:

#include "tip4p.itp"
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
    1    1       1000       1000       1000

where it is a per-molecule atomic index definition such that "atom 1"  
is applied to each solvent molecule.

If you are still unclear, I strongly suspect that there is a gmx  
manual description of all of this, and suggest that you read the  
manual in search of it. If you can't find one then probably you should  
complain back to this list about the absence of a section that should  
definitely be there.


-- original message --

From: Morteza Khabiri <khabiri at greentech.cz>
Subject: [gmx-users] POSITION-RESTRAIN
To: gmx-users at gromacs.org
Date: Monday, 27 July, 2009, 7:35 PM

Dear gmxusers.

I want to restrain the lipids in my system which contains protein,lipid
and water. I make the restraint itp file by genpr then I added it in
toplogy file.
After doing grompp to make tpr file I get the following message:

Fatal error:
[ file "posre_entirelipid1.itp", line 56 ]:
              Atom index (53) in position_restraints out of bounds (1-52)
I found the similar error in the mailing list and they suggested probably
the place of restraint itp file which was included in  topology file is
wrong.  However, I tried several positions for restraint itp but I think
it is not the
solution. Do you have any other suggestion about this problem??????


Mark is right.....the position restrain.itp file should be included in  
your topology file in the proper place otherwise the problem would  
continue. place the .itp file after the section
; Include Position restraint file

#ifdef POSRES

#include "posre.itp"


best wishes

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