[gmx-users] Water molecule can not be settled

[zeineb SI CHAIB]

Dear gmx users, 

I'm having problems during my energy minimisation step, I tried different options in the mdp file but I'm enable to fix the problem, I'm hoping that you can help me with this. 

My system is a dimer that contain HEM, cofactor (Tetrahydrofolate, THF) and arginin (substrate). I'm using CHARMM27 as a force field. 

At the beginning I fixed the problem of the HEM (perfectly linked with the protein and completed its parameters).
In the second step, I generated the topology of THF with Swissparam's server. I succeeded in running a molecular dynamic of 5ns. When I analysed the dynamic the THF was in its right place and I didn't see any anormal behaviour with my structure. 

Now, I'm trying to include the topology of the THF in CHARMM ff folder in order to gain time and make things  more automatic. The modifications that I did were:
- I added the residue to the .rtp file of CHARMM FF, only  [atoms] entry.  
For the other entries [angles], [impropres]..etc, according to GROMACS manual, they are optional so I did'nt add them. 

- I created an entry for THF in the .hdb file of CHARMM ff. 

After that, I run pdb2gmx and it succeeded to generate the topology. The global structure looked OK but during energy minimisation, I got this Fatal error:

Fatal error:
step 36: Water molecule starting at atom 15431 can not be settled.
The atom 15431 belong to a water molecule and is far from the protein!!


Here are the parameters that I used in the mdp file:
integrator = steep  
nsteps = 50000   
nstxout = 1  
ns_type = grid 
energygrps  = Protein THG 
emtol = 1000.0  
emstep = 0.01  

; Non bonded stuff (specific to CHARMM)  
constraints = h-bonds
cutoff-scheme = Verlet
vdwtype = cutoff
vdw-modifier = force-switch
rlist = 1.2
rvdw = 1.2
rvdw-switch = 1.0
coulombtype = PME
rcoulomb = 1.2
DispCorr = no

I tried to change the parameters (one changement each time) but it didn't work:
1- define = DFLEXIBLE
2- define = DEPOSRE
3- constraints = all-bonds 
4- emstep = 0,02

I can't see where is the problem! Anyone can help me please.

Regards. 

Zeineb