Please do tell me if this is what you were searching....

Hope it helps...

Regards,

http://rashmikumari.github.io/g_mmpbsa/single_protein_ligand_energy_contributions.html

Try to use the following scripts and see if any changes happen.

In order to put restraint during Partial minimization step and heating step you have to holdthe proteins fixed the input file. See below the input files

Input of Partial minimization

# Res 1 198 describes residue number in case protein+ligand complex. E.g. in case of inhibitor bound HIV-protease the total residue number for receptor is 198 and the ligand is 1. Thus total residue count 198+1=199. You can hold the system by mentioning residue numbers

Initial minimization of MMP3 (MMMM): solvent molecules and added ions

&cntrl

imin = 1,

maxcyc = 2500,

ncyc = 750,

ntb = 1,

ntr = 1,

cut = 12.0,

/

Hold the Protein fixed

10.0

RES 1 199

END

END

Input for Full minimization

Full minimization of MMP3 (MMMM): protein, ligand, solvent molecules and added ions

&cntrl

imin = 1,

maxcyc = 200,

ncyc = 50,

ntb = 1,

ntr = 0,

cut = 12.0,

Drms = 0.0001,

/

END

Input for Heating stage

#tempi(temperature input)=0 (0K); tempo(temperature output)=300 (300K)

#Res 1 199 is similar to the explanation provided above

Heating Step of MMP3 (MMMM): stage-5

&cntrl

imin= 0,

irest=1,

NTX=1,

ntb= 1,

NTPR=500,

NTWX=500,

NTWR=500,

ntr=1,

Tempi=0.0,

Temp0=300.0,

NTT=3,

gamma_ln=1.0,

NTC=2,

NTF=2,

cut= 12.0,

nstlim=2500,

dt=0.002,

/

Keep Protein and inhibitor fixed with weak restraints

10.0

RES 1 557

END

END

Input for Equilibration stage

Equilibration Step of MMP3 (MMMM): stage-1

&cntrl

imin= 0,

irest=1,

NTX=7,

ntb=2,

ntp=1,

PRES0=1.0,

TAUP=2.0,

NTPR=500,

NTWX=500,

ntr=0,

Tempi=300.0,

Temp0=300.0,

NTT=3,

gamma_ln=1.0,

NTC=2,

NTF=2,

cut=12.0,

nstlim=250000,

dt=0.002

/

Input for MD production stage

#change nstlim as per simulation time (nstlim is number of steps). 5ns=2500000 (nstlim)

Equilibration Step of MMP3 (MMMM): stage-1

&cntrl

imin= 0,

irest=0,

ig=-1,

NTX=7,

ntb=2,

ntp=1,

PRES0=1.0,

TAUP=2.0,

NTPR=500,

NTWX=500,

ntr=0,

Tempi=300.0,

Temp0=300.0,

NTT=3,

gamma_ln=1.0,

NTC=2,

NTF=2,

cut=12.0,

nstlim=2500000,

dt=0.002

/

Give atleast 10ns equilibration period prior to simulation. In order to remove any Imaging artifact use the following script to generate stripped topology and co-ordinate files

#specifying the input .mdcrd file

trajin md50.mdcrd

#stripping water and Cl- and creating a com_solvated.top with a prefix stripped

strip :WAT,Cl- out prefix stripped

# to generate a stripped image of com_solvated.top

autoimage

#dry .mdcrd files

trajout md50_dry.mdcrd

Execute like ~/amber12/bin/cpptraj com_solvated.top strip.ptrj

Upload the stripped topology and dry_mdcrd file in Chimera or VMD to view the movie.

Hope this much helps. You can access full tutorial here https://cbiores.wordpress.com/simulation-with-amber/

 Hope it helps.

Cheers!!

Observations of one simulation is very dangerous to interpret. What you are observing during simulations might be some stochastic event. If you would find same event in several simulations, then you may interpret it. Therefore, I would suggest to do multiple simulations.

Performing multiple simulations will help in this work, however, restraining through out the production run is the better choice to interpret the correct results. Further, you may try restraining different parts in multiple simulations.

I would not restrain during production phase. If ligand is moving, it might be another conformational state of the system, and this can be confirmed only by multiple simulations. Another issue might be the force-field, I would also check differences in ligands.  For example, protonation states, halogen atoms etc.