blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Hi Would you please help me how can i solve my problem ? I wanna
to do equilibrate my complex ( 4ly1 + ligand) but when use the nvt.mdp file in
protein -ligand complex (lysosym4) tuturial in gromacs , i faced to an error:
step 1: One or more water molecules can not be settled. Check for bad contacts
and/or reduce the timestep if appropriateThanks alotFarial
Sent from Yahoo Mail for iPhone
Begin forwarded message:
On Wednesday, July 5, 2017, 6:31 PM, farial tavakoli
<farial.tavak...@ymail.com> wrote:
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)
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