[gmx-users] freez few residues in protein

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Dear gmx users,


I wan to freez few residues in protein, therefore i have listed those numberst in ndx and mdp file. The energy minimization was done well and its freezes the residues as i listed out. However, when i start NVT with same way, it shows following error.


Fatal error:
Group Protein referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp.






Please help me out in this issue. Thanks.




These are my ndx and mdp file :


eg : ndx file


[ g1 ]
  28   29   30   31   32   33   34   35   36   37 
[ g2 ]
  74   75   76   77   78   79   80   81   82   83   84   85 
[ g3 ]
 241  242  243  244  245  246  247  248  249  250  251  252 


my NVT mdp file:


 title		        = NVT equilibration 
define		= -DPOSRES	; position restrain the protein
; Run parameters
integrator	        = md		; leap-frog integrator
nsteps		= 50000		; 2 * 50000 = 100 ps
dt		        = 0.002		; 2 fs
; Output control
nstxout		= 100		; save coordinates every 0.2 ps
nstvout		= 100		; save velocities every 0.2 ps
nstenergy	= 100		; save energies every 0.2 ps
nstlog		= 100		; update log file every 0.2 ps
; Bond parameters
continuation	= no		        ; first dynamics run
constraint_algorithm = lincs	; holonomic constraints 
constraints	= all-bonds	; all bonds (even heavy atom-H bonds) constrained
lincs_iter   	= 1		        ; accuracy of LINCS
lincs_order	= 4		        ; also related to accuracy
; Neighborsearching 
ns_type		= grid		; search neighboring grid cells
nstlist		= 5		        ; 10 fs
rlist		        = 1.0		; short-range neighborlist cutoff (in nm)
rcoulomb	        = 1.0		; short-range electrostatic cutoff (in nm)
rvdw		        = 1.0		; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype	= PME		; Particle Mesh Ewald for long-range electrostatics
pme_order	= 4		        ; cubic interpolation
fourierspacing	= 0.16		; grid spacing for FFT
; Temperature coupling is on
tcoupl		= V-rescale	; modified Berendsen thermostat
tc-grps		= Protein Non-Protein	; two coupling groups - more accurate
tau_t		= 0.1	0.1	; time constant, in ps
ref_t		        = 300 	300	; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl		= no 		; no pressure coupling in NVT
; Periodic boundary conditions
pbc		        = xyz		; 3-D PBC
; Dispersion correction
DispCorr	        = EnerPres	; account for cut-off vdW scheme
; Velocity generation
gen_vel		= yes		; assign velocities from Maxwell distribution
gen_temp	= 300		; temperature for Maxwell distribution
gen_seed	= -1		       ; generate a random seed
freezegrps      = g1 g2 g3 g4 g5 g6 g7 g8 g9 g10 g11 g12 g13 g14 g15 g16 g17 g18 g19 g20 g21 g22 g23 g24 g25 g26 g27 g28 g29    
freezedim       =  Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y