HiI am a new GROMACS user and trying to run md on HDAC2 with PDB ID: 4LY1. but when I wanted to performance equilibration , i got this ERROR: step 1: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate
Would you please help me to fix this problem? These are all stages which I did: I took 4LY1.pdb file from PDB site and removed B and C chains and all ligands and water molecules from it and left just chain A and HETATM ZN A . I constructed my protein topology by using gromos 43a1 and this command:pdb2gmx -f 4LY1.pdb -o 4LY1.gro -water spc then made a complex.gro file which include 4LY1.gro and DRG.gro which i got from PRODRG site. I also copy paste ; Include ligand topology #include "DRG.itp" in the topology file and added DRG as a ligand in [ molecules ] directive. Then I defined box by using this command : gmx editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.0 then defined solvate by : gmx solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro then used grommp to assemble a .tpr file by using a .mdp file and this command : gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr that was my .mdp afile : 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 and added 2 CL ions since my total charge was 2.00 because of zn ion. gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -nn 2 then for minimization, i replaced energygroups from system to protein DRG in em_real.mdp. that was my em_real.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 = protein DRG ; 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 and typed these command: gmx grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o em.tpr and gmx mdrun -v -deffnm em GROMACS replies: Steepest Descents converged to Fmax < 1000 in 1833 steps Potential Energy = -5.6356275e+05 Maximum force = 9.7815100e+02 on atom 3452 Norm of force = 3.1465845e+01 Simulation ended prematurely, no performance report will be written. Is there any problem that simulation ended prematurely? Then for equilibriation i typed gmx genrestr -f jz4.gro -o posre_jz4.itp -fc 1000 1000 1000 and in order to restrain both the protein and the ligand simultaneously, I specify define = -DPOSRES -DPOSRES_LIG in the .mdp file. then typed gmx make_ndx -f em.gro -o index.ndx to merge the protein and DRG. and selected protein and DRG by : > 1 | 14 > qthen set tc_grps = Protein_DRG Water_and_ions in NVT.mdp file to achieve my > desired "Protein Non-Protein" effect. that was my NVT.mdp file: title = Protein-ligand complex NVT equilibration define = -DPOSRES -DPOSRES_LIG ; position restrain the protein and ligand integrator = md ; leap-frog integratornsteps = 50000 ; 2 * 50000 = 100 psdt = 0.002 ; 2 fs; Output controlnstxout = 500 ; save coordinates every 1.0 psnstvout = 500 ; save velocities every 1.0 psnstenergy = 500 ; save energies every 1.0 psnstlog = 500 ; update log file every 1.0 psenergygrps = Protein DRG; Bond parameterscontinuation = no ; first dynamics runconstraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrainedlincs_iter = 1 ; accuracy of LINCSlincs_order = 4 ; also related to accuracy; Neighborsearchingcutoff-scheme = Verletns_type = grid ; search neighboring grid cellsnstlist = 10 ; 20 fs, largely irrelevant with Verletrcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)rvdw = 1.4 ; short-range van der Waals cutoff (in nm); Electrostaticscoulombtype = PME ; Particle Mesh Ewald for long-range electrostaticspme_order = 4 ; cubic interpolationfourierspacing = 0.16 ; grid spacing for FFT; Temperature couplingtcoupl = V-rescale ; modified Berendsen thermostattc-grps = Protein_DRG Water_and_ions ; two coupling groups - more accuratetau_t = 0.1 0.1 ; time constant, in psref_t = 300 300 ; reference temperature, one for each group, in K; Pressure couplingpcoupl = no ; no pressure coupling in NVT; Periodic boundary conditionspbc = xyz ; 3-D PBC; Dispersion correctionDispCorr = EnerPres ; account for cut-off vdW scheme; Velocity generationgen_vel = yes ; assign velocities from Maxwell distributiongen_temp = 300 ; temperature for Maxwell distributiongen_seed = -1 ; generate a random seed then i typed these commands: gmx grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr and gmx mdrun -deffnm nvt but GROMACS replied : step 1: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step1b.pdb to ./#step1b.pdb.19# Back Off! I just backed up step1c.pdb to ./#step1c.pdb.19# Wrote pdb files with previous and current coordinates Segmentation fault (core dumped) -- 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.