Maybe you are applying the restraint on the backbone atoms. Double-check the definition mdp file as well is topol.

Ishrat Jahan

Usually is recommended adding some restraint to those residues coordinating the metal ion since classical force fields can't describe accurately the coordination geometry. Restraint can be either on position or distances...

hope this helps!

Thanks for the reply Mario E. Valdés-Tresanco and Nikhil Maroli . Kindly check my mdp and top file provided below-

full.mdp:

;

; User spoel (236)

; Wed Nov 3 17:12:44 1993

; Input file

;

title = Yo

define = -DPOSRES

cpp = /usr/bin/cpp

constraints = all-bonds

constraint-algorithm= Lincs

integrator = md

dt = 0.002 ; ps !

nsteps = 500000 ; total 500000 ps.

nstcomm = 100

nstxout = 100

nstvout = 100

nstfout = 0

nstlog = 5000

nstenergy = 5000

nstxtcout = 5000

nstlist = 10

ns_type = grid

rlist = 1.2

coulombtype = PME

rcoulomb = 1.2

rvdw = 1.2

fourierspacing = 0.12

fourier_nx = 0

fourier_ny = 0

fourier_nz = 0

pme_order = 4

ewald_rtol = 1e-5

optimize_fft = yes

; Berendsen temperature coupling is on in two groups

Tcoupl = V-rescale

tc-grps = Protein Ion SOL

tau_t = 0.1 0.1 0.1

ref_t = 300 300 300

; Energy monitoring

energygrps = Protein Ion SOL

; Isotropic pressure coupling is now on

Pcoupl = berendsen

Pcoupltype = isotropic

tau_p = 0.5

compressibility = 4.5e-5

ref_p = 1.0

refcoord_scaling = com

; Generate velocites is off at 300 K.

gen_vel = no

gen_temp = 300.0

gen_seed = 173529

and position restraints part of top file ;

Include water topology

#include "gromos53a5.ff/spc.itp"

#ifdef POSRES_WATER

; Position restraint for each water oxygen

[ position_restraints ]

; i funct fcx fcy fcz

1408 1 1000 1000 1000

1409 1 1000 1000 1000

#endif

Dposres is default position restrain file name for protein chain(if you don't change) so I guess you restraining both molecule. Give specific name for metal restrain file and use it.

If you are not getting it share both mdp and topol file.

Thanks, I get it.