[gmx-users] DispErsion correction

[Farial Tavakoli]

Dear Justin and Dallas

Thank you for your replying

I have another problem in minimizing and NVT run of my complex, including a
protein and a peptidic ligand which the ligand has 2 phosphotyrosine
residues. I generated a topology file of ligand using ff14sb in ambertools
16 and then converted the .inpcrd and .prmtop files in .gro and .top files
using acpype python script. The protein topology was generated using
amber99sb ff in GROMACS.
Then, I cited to gromacs manuscript in order to generate an .itp file of
ligand from .top file and generated .itp file by removing the header and
footer of .top file in such a way that .itp file starts with :
[ moleculetype ]
;name            nrexcl
 mig               3

[ atoms ]
;   nr  type  resi  res  atom  cgnr     charge      mass       ; qtot
bond_type
     1   N3     1   THR     N    1     0.181200     14.01000 ; qtot 0.181
     2    H     1   THR    H1    2     0.193400      1.00800 ; qtot 0.375
.
.
.
and ends with
    120    123    122    132      1   180.00   4.18400   2 ;      C-
CD-     N-    CA
   132    135    134    136      1   180.00  43.93200   2 ;     CA-
O-     C-   OXT
then, modified the complex.gro and .top files according to the tutorials in
gromacs, I Minimized the complex by issuing this coomand:
gmx grompp -f em.mdp -c solv-ions.gro -p topol.top -o em.tpr
gmx mdrun -v -defnm em
but noticed that the minimization ended soon :

Steepest Descents converged to machine precision in 80 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -6.5639856e+05
Maximum force     =  7.0647156e+04 on atom 5256
Norm of force     =  5.8775842e+02

and when performed the NVT run , faced to this error:

starting mdrun 'Protein in water'
200000 steps,    400.0 ps.
step 0
Step 5, time 0.01 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.016999, max 0.734404 (between atoms 5258 and 5261)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   5258   5261   90.0    0.0960   0.1665      0.0960
   5283   5286   90.0    0.0960   0.1425      0.0960
Wrote pdb files with previous and current coordinates
.
.
.
It should be noted that atoms 5258 and 5261 are related to sol molecules.
TIP3P water model was selected for amber99sb force field.
Would you please advice and guild me how should I resolve this problem?

Thanks in advance
Farial


these are the .mdp files that I used:
em.mdp file:
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator  = steep         ; Algorithm (steep = steepest descent
minimization)
emtol       = 1000.0        ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
emstep      = 0.01          ; Minimization step size
nsteps      = 50000         ; Maximum number of (minimization) steps to
perform

; 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    ; Buffered neighbor searching
ns_type         = grid      ; Method to determine neighbor list (simple,
grid)
coulombtype     = PME       ; Treatment of long range electrostatic
interactions
rcoulomb        = 1.0       ; Short-range electrostatic cut-off
rvdw            = 1.0       ; Short-range Van der Waals cut-off
pbc             = xyz       ; Periodic Boundary Conditions in all 3
dimensions


the nvt.mdp file:
title                   = AMBER  NVT equilibration
define                  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator              = md        ; leap-frog integrator
nsteps                  = 200000     ; 2 * 200000 = 400 ps
dt                      = 0.002     ; 2 fs
; Output control
nstxout                 = 500       ; save coordinates every 1.0 ps
nstvout                 = 500       ; save velocities every 1.0 ps
nstenergy               = 500       ; save energies every 1.0 ps
nstlog                  = 500       ; update log file every 1.0 ps
; Bond parameters
continuation            = no        ; first dynamics run
constraint_algorithm    = lincs     ; holonomic constraints
constraints             = h-bonds   ; bonds involving H are constrained
lincs_iter              = 1         ; accuracy of LINCS
lincs_order             = 4         ; also related to accuracy
; Nonbonded settings
cutoff-scheme           = Verlet    ; Buffered neighbor searching
ns_type                 = grid      ; search neighboring grid cells
nstlist                 = 10        ; 20 fs, largely irrelevant with Verlet
rcoulomb                = 1.0       ; short-range electrostatic cutoff (in
nm)
rvdw                    = 1.0       ; short-range van der Waals cutoff (in
nm)
; Electrostatics
coulombtype             = PME       ; Particle Mesh Ewald for long-range
electrostatics
pme_order               = 4         ; cubic interpolation
fourierspacing          = 0.16      ; grid spacing for FFT
; Temperature coupling is on
tcoupl                  = V-rescale             ; modified Berendsen
thermostat
tc-grps                 = Protein Non-Protein   ; two coupling groups -
more accurate
tau_t                   = 0.1     0.1           ; time constant, in ps
ref_t                   = 300     300           ; reference temperature,
one for each group, in K
; Pressure coupling is off
pcoupl                  = no        ; no pressure coupling in NVT
; Periodic boundary conditions
pbc                     = xyz       ; 3-D PBC
; Velocity generation
gen_vel                 = yes       ; assign velocities from Maxwell
distribution
gen_temp                = 300       ; temperature for Maxwell distribution
gen_seed                = -1        ; generate a random seed