Samik Bhattacharya samikbhat at yahoo.co.in
Tue Jul 28 03:57:44 CEST 2009

--- On Mon, 27/7/09, Morteza Khabiri <khabiri at greentech.cz> wrote:

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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