[gmx-users] where to insert a new include DPOSRES in topology file?

Anna Marabotti anna.marabotti at isa.cnr.it
Fri Feb 18 11:54:13 CET 2011

Dear all,
I would like to do a position restraint MD by applying position restraints
not only to my protein but also to its ligand. In order to do it, I created
with genrestr a new protligposre.itp file in which I indicated the group to
be restrained as Protein_lig. In this protligposre.itp file, therefore,
there are restraints on the protein and on the ligand together.
Then, I modified the .top file in order to include the statement for the
position restraints. I tried to modify first the usual statement:
#ifdef POSRES
#include 'posre.itp'
#include 'protligposre.itp'
(obviously, in my .mdp file I have the statement define = -DPOSRES_PROTLIG)
Since it did not work, I used:
#ifdef POSRES
#include "protligposre.itp"
(obviously, the statement in the .mdp file was modified to -DPOSRES)
Then, I tried to ADD (not to replace) a new 
#include "protligposre.itp"
and I tried all the positions in the .top file. 
Every time, I obtained an error stating:
Fatal error: 
[file protligposre.itp, line 2822 (this number changes every time I change
the position of the statement in the .top file)
Atom index (2818) in position_restraints out of bounds (1-2817).
This probably means that you have inserted topology section
"position_restraints" in a part belonging to a different molecule that you
intended to. In that case, move the "position_restraints" section to the
right molecule.
I really don't know what is the correct position for this statement, since I
tried all position that I could, starting just below the already present
Moreover, another doubt I have is: is it correct to include protein and
ligand in the same posre.itp file? In case it is not correct, what is the
correct position in the .top file to insert the ligposre.itp file (the file
containing position restraints for ligand only)? Please consider that in my
.top file the topology of the ligand was added with the statement
#include "lig.itp"
just below the statement for the forcefield.
Thank you very much
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science - CNR
Via Roma, 64
83100 Avellino
Phone: +39 0825 299651
Fax: +39 0825 781585
E-mail: amarabotti at isa.cnr.it
Skype account: annam1972
Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
"When a man with a gun meets a man with a pen, the man with the gun is a
dead man"
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