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"
#ifdef POSRES_SOL
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
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.
Chris.
-- 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??????
Thanks
hi,
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"
#endif
best wishes
Shamik
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