[gmx-users] ligan minimization in vacuo

[‪farial tavakoli‬ ‪]

Dear gmx-users
I have a problem in equilibration my protein-ligand complex and encountered to this error after 2 steps of 50000 steps:one or more water molecules can not be settled. check for bad contacts or reduce the time steps. 
so I decided to create a topology for my designed drug (50 atoms) as a ligand to minimize it in the vacuo in the absence of the protein to check if it minimizes  , so i tried to change the .itp file obtained from PRODRG to create a .top file,  in this way:I added  " ; Include forcefield parameters
    #include "gromos43a1.ff/forcefield.itp " above the [ moleculetype ] directive as a first line , then added [ system ] and [ molecule ] directives under the ligand, respectively :
  23  24  26  27   1    180.0   33.5 2    180.0   33.5 2 ; dih   CAS  CAR  NAQ  CAN   
  32  27  26  24   1    180.0   33.5 2    180.0   33.5 2 ; dih   CAM  CAN  NAQ  CAR   
  39  37  36  30   1    180.0    5.9 2    180.0    5.9 2 ; dih   SAG  CAH  CAK  CAP   
  40  48  49  50   1    180.0    7.1 2    180.0    7.1 2 ; dih   CAA  CAF  OAJ  HAJ

; Ligand position restraints
#ifdef POSRES
#include "posre_DRG.itp"
#endif

; Include water topology
#include "gromos43a1.ff/spc.itp"

[ system ]
; Name
DRG in water

[ molecules ]
; Compound        #mols
DRG                      1
issued this command:gmx grompp -v -f em.mdp -c DRG.gro -p DRG.top -o DRG-EM-vacuum.tprgmx mdrun -v -deffnm DRG-EM-vacuum -c DRG-EM-vacuum.gro 
and simulation results:
Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =        50000
Step=    0, Dmax= 1.0e-02 nm, Epot=  1.41636e+03 Fmax= 2.81150e+04, atom= 25
Step=    1, Dmax= 1.0e-02 nm, Epot=  1.01416e+03 Fmax= 1.21118e+04, atom= 25
Step=    2, Dmax= 1.2e-02 nm, Epot=  7.87016e+02 Fmax= 4.71639e+03, atom= 25
Step=    3, Dmax= 1.4e-02 nm, Epot=  6.94638e+02 Fmax= 5.88719e+03, atom= 15
Step=    5, Dmax= 8.6e-03 nm, Epot=  6.79808e+02 Fmax= 7.13390e+03, atom= 15
Step=    7, Dmax= 5.2e-03 nm, Epot=  6.29169e+02 Fmax= 1.31714e+03, atom= 25
Step=    8, Dmax= 6.2e-03 nm, Epot=  6.12279e+02 Fmax= 2.91712e+03, atom= 14
Step=   10, Dmax= 3.7e-03 nm, Epot=  6.04849e+02 Fmax= 2.77294e+03, atom= 27
Step=   12, Dmax= 2.2e-03 nm, Epot=  5.86062e+02 Fmax= 9.77798e+02, atom= 24

writing lowest energy coordinates.

Back Off! I just backed up DRG-EM-vacuum.gro to ./#DRG-EM-vacuum.gro.1#

Steepest Descents converged to Fmax < 1000 in 13 steps
Potential Energy  =  5.8606232e+02
Maximum force     =  9.7779791e+02 on atom 24
Norm of force     =  3.8248090e+02

Simulation ended prematurely, no performance report will be written.


 here's my em.mdp file:

integrator      = steep        ; Algorithm (steep = steepest descent minimization)
emtol            = 1000.0      ; Stop minimization when the maximum force < 10.0 kJ/mol
emstep         = 0.01         ; Energy step size
nsteps          = 50000       ; Maximum number of (minimization) steps to perform
energygrps    = system    ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist               = 1            ; Frequency to update the neighbor list and long range forces
cutoff-scheme   = Verlet
ns_type            = grid        ; Method to determine neighbor list (simple, grid)
rlist                  = 1.0        ; Cut-off for making neighbor list (short range forces)
coulombtype     = PME      ; Treatment of long range electrostatic interactions
rcoulomb          = 1.0        ; long range electrostatic cut-off
rvdw                = 1.0        ; long range Van der Waals cut-off
pbc                 = xyz        ; Periodic Boundary Conditions

I just wanted to know if I did correct?In addition after minimization in vacuo , checked my ligand in pymol and noticed it is disintegrated.  Is there anyone help me how come it is disintegrated ,however i edited the .itp file obtained from PRODRG ( charges and charg groups)? How can i fix this problem to equilibrate my complex? 


 thank you in advance 
Farial