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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.