[gmx-users] atoms are not part of any of the T-Coupling groups

[Nidhi Katyal]

Hello all,

I am working on protein with two chains. I would like to restrain one atom
of one chain while doing steered MD. For the same reason, I have created an
index file that includes that atom, then created its posre.itp file and
finally included following lines at the end of topol_Protein_chainA.itp:

; Include Position restraint file
#ifdef POSRES_CA_chA_r131
#include "posre.itp"
#endif

I am also pasting a small section of my topol.top file:


; Include forcefield parameters
#include "gromos53a6.ff/forcefield.itp"

; Include chain topologies
#include "topol_Protein_chain_A.itp"
#include "topol_Protein_chain_B.itp"
#include "topol_Ion_chain_A2.itp"
#include "topol_Ion_chain_B2.itp"

; Include water topology
#include "gromos53a6.ff/spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

After carrying out NPT equilibration, when I run following command:

grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt
-o pull.tpr

as given in tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html

I am getting following error:
215400 atoms are not part of any of the T-Coupling groups

Since my pull.mdp file as the same as given in tutorial, my coupling
groups are Protein and Non-Protein.
I suspect there is something wrong while adding restraints using
include file mechanism. Please help me resolve the problem.

Thanks
Nidhi